Marker sequences for diagnosing and stratifying sle patients

ABSTRACT

The present invention relates to methods for identifying markers for systemic lupus erythematosus (SLE) and to the markers identified with the aid of this method, which can differentiate between SLE and other autoimmune diseases on the one hand and between different SLE subgroups on the other hand. The invention also relates to panels, diagnostic devices and test kits which comprise these markers, and to the use and application thereof, for example for the diagnosis, prognosis and therapy control in SLE. The invention also relates to methods for screening and validating active substances for application in SLE subgroups.

The present application is being filed along with a Sequence Listing inelectronic format. The Sequence Listing is provided as a file entitled16920949_SequenceListing, created Sep. 30, 2020, which is 6,549,888bytes in size. The information in the electronic format of the sequencelisting is incorporated herein by reference in its entirety.

The present invention relates to methods for identifying markers forsystemic lupus erythematosus (SLE) and to the markers identified withthe aid of this method, which can differentiate between SLE and otherautoimmune diseases on the one hand and between different SLE subgroupson the other hand. The invention also relates to panels of markers forSLE, diagnostic devices and test kits for SLE which comprise thesemarkers, and to the use and application thereof, for example for thediagnosis, prognosis and therapy control of SLE. The invention alsorelates to methods for screening and for validating active substancesfor application in SLE subgroups.

Systemic lupus erythematosus (SLE) is a rare autoimmune disease. In thecase of lupus erythematosus the body's own immune system isdisregulated. It not only attacks bacteria, viruses and cancer cells,but also healthy body cells. Organs and organ systems, for example theskin, are damaged as a result.

In clinical practice, SLE is diagnosed on the basis of a combination ofclinical and immunological parameters. Here, antinuclear autoantibodies(ANAs) and anti-double-stranded DNA (anti-dsDNA) autoantibodies play akey role. However, the ANA test is not specific for SLE, since otherautoimmune diseases and up to 20% of healthy individuals are alsopositively tested. The autoreactivity against extractable nuclearantigens (EMAs) as recombinant or purified individual antigens istherefore increasingly tested, for example against Sm-protein, U1-RNP,Rho52/SS-A and Ro60/SS-B. These antigens and associated autoantibodies,however, are not sufficient for diagnosing all SLE patients withoutdoubt, in particular in an early phase of the disease. By way ofexample, anti-dsDNA antibodies are indeed highly specific for SLE andcan be detected in approximately 70% of patients. However, the titre ofthe anti-dsDNA antibodies correlates with the disease activity in somepatients, but not in all patients. As a result, SLE is often onlydiagnosed months or years after the occurrence of the first symptoms. Afurther problem of the currently used diagnostic methods is that thesuitability of the previously tested autoantigens for the diagnosis oforgan involvement and complications is disputed, and partly conflictingdata has been published.

There is thus a great need to provide new markers for the diagnosis anddifferential diagnosis of SLE.

Marker sequences for the diagnosis of SLE are disclosed in WO2012/0-19225 A2. These marker sequences were discovered by a method inwhich serum samples of SLE patients and those of healthy individualswere examined by comparison and the results were statisticallyevaluated. The marker sequences described in WO 2012/049225 A2, however,are not sufficiently suitable for the diagnosis of SLE with regard to adistinction from other autoimmune diseases and the identification of SLEsubgroups.

There is therefore still a need for markers for SLE, in particular forthe distinction of SLE from other autoimmune diseases.

This object has been achieved in accordance with the invention in that adifferential method comprising a multiplicity of steps has beendeveloped, in which serum samples of healthy individuals and patientswith various autoimmune diseases were examined by comparison with,regard to their reactivity with a multiplicity of potential antigens andthese results were statistically evaluated. The selection of the serumsamples and the sequence of the steps surprisingly made it possible toidentify highly specific markers for SLE which are also suitable foridentifying SLE subgroups and complications such as lupus nephritis andfor providing a differential diagnosis in respect of other autoimmunediseases, such as rheumatoid arthritis (RA), systemic sclerosis (SSc),ankylosing spondylitis or Bekhterev's disease (SPA), and also in respectof individuals who have early RA, i.e. have been suffering with thedisease for less than two years (“patients with early RA”).

The present invention relates to a method for identifying markers forsystemic lupus erythematosus (SLE) comprising the following steps

-   -   a) bringing serum samples of SLE patients into contact with more        than 5000 antigens coupled to (Luminex) heads, measuring the        binding of the individual antigens to proteins, in particular        autoantibodies, in the serum of the SLE patients by means of        immunofluorescence assay, and determining the median        fluorescence intensity (MFI) for each individual antigen;    -   b) bringing serum samples of patients with rheumatoid arthritis        (RA) into contact ‘with the same antigens coupled to (Luminex)        beads, measuring the binding of the individual antigens to        proteins, in particular autoantibodies, in the serum, of the RA        patients by means of immunofluorescence assay, and determining        from this the median fluorescence intensity (MFI) for each        individual antigen;    -   c) bringing serum samples of healthy individuals into contact        with the same antigens coupled to (Luminex) beads, measuring the        binding of the individual antigens to proteins, in particular        autoantibodies, in the serum of the healthy individuals by means        of immunofluorescence assay, and determining from this the        median, fluorescence intensity (MFI) for each individual        antigen;    -   d) statistically evaluating the MFI data from a), b) and c) by        means of univariate analysis and thus identifying marker        candidate antigens with which SLE patients can be differentiated        from RA patients and from healthy individuals;    -   e) bringing serum samples of patients with early RA. into        contact, with the marker candidate antigens identified in d)        coupled to (Luminex) beads, measuring the binding of marker        candidate antigens to proteins, in particular autoantibodies, in        the serum of patients with early RA by means of        immunofluorescence assay, and determining from this the median        fluorescence intensity (MFI) for each marker candidate antigen;    -   f) bringing serum samples of patients with systemic sclerosis        (SSc patients) into contact with the marker candidate antigens        identified in d) coupled to (Luminex) beads, measuring the        binding of marker candidate antigens to proteins, in particular        autoantibodies, in the serum of SSc patients by        immunofluorescence assay, and determining from this the median        fluorescence intensity (MFI) for each marker candidate;    -   g) bringing serum samples of patients with ankylosing        spondylitis or Bekhterev's disease (SPA patients) into contact        with the marker candidate antigens identified in d) coupled to        (Luminex) beads, measuring the binding of marker candidate        antigens to proteins, in particular autoantibodies, in the serum        of SPA patients by means of immunofluorescence assay, and        determining from this the median fluorescence intensify (MFI)        for each marker candidate antigen;    -   h) statistically evaluating the MFI data from e), f) and g) by        means of univariate analysis and, when a threshold value of 3        standard deviations above the mean value of the healthy samples        is not reached, identifying a specific marker for SLE, wherein        the markers are selected from sequences SEQ ID No. 1 to 1587,        homologues of sequences SEQ ID No. 1 to 1587 with at least 95%        homology, subsequences of SEQ ID No. 1 to 1587, subsequences of        homologues of SEQ ID No. 1 to 1587 with at least 95% homology.

The term “systemic lupus erythematosus (SLE) relates to a systemicautoimmune disease from the group of collagenoses. What is known as thebutterfly rash is particularly characteristic for SLE (systemic lupuserythematosus). The diagnosis criteria for SLE are:

1. butterfly rash, 2. discoid skin changes, 3. sensitivity to light, 4.mucous membrane ulcers (generally painless), 5. arthritis in at leasttwo joints, 6. serositis (pleurisy or pericarditis), 7. kidneyinvolvement (proteinuria>0,5 g/d or cylinder), 8. CNS involvement(cramps or psychosis), 9. haematological findings (haemolytic anaemia,leucopenia or thrombopenia), 10. immunological findings (anti-dsDNAantibodies, anti-Sm antibodies, anticardiolipin antibodies), 11.antinuclear antibodies without taking lupus erythematosus-triggeringmedication.

Evaluation: With four (three) positive findings, the diagnosis isconsidered reliable (likely) (definition for example according toPschyrembei, de Gruyter, 261st edition (2007), Berlin),

One embodiment of the invention relates to methods for identifyingmarkers for SLE which are suitable for the diagnosis and differentialdiagnosis of SLE, in. particular for distinction from other autoimmunediseases, preferably for distinction from, other rheumatic diseases,particularly preferably for distinction from RA, SSc, and SPA. Thesemarkers are also suitable for distinction from patients with early RA,These markers for SLE according to the invention are the subject ofgroup 1 of antigens in Table 2, which can be used for the diagnosis ofSLE. For the generation of these markers, marker candidate antigenswhich have an adjusted p-value for the non-parametric mean valuecomparison between groups of <0.05 and at the same time a fold changeof >1.5 and additionally an AUC resulting from the ROC analysis of >0.75are selected on the basis of the univariate results. In addition, theENA-4 antigens are selected. For this pool of selected marker candidateantigens, an L1-penalised logistic regression model is preferably alsoestablished within the scope of a nested cross validation. Markercandidate antigens which are not considered within the scope of thecreation of the model are removed from the further consideration. Themarkers for SLE are thus obtained, selected from the sequences (group 1)

SEQ ID No. 1 to 24, 134, 168, 214, 368 to 370 SEQ ID No. 530 to 553,663, 697, 743, 897 to 899 and SEQ ID No. 1059 to 1082, 1192, 1226, 1272,1426 to 1428, homologues of SEQ ID No. 1 to 24, 134, 168, 214, 368 to370 SEQ ID No. 530 to 553, 663, 697, 743, 897 to 899 and SEQ ID No. 1059to 1082, 1192, 1226, 1272, 1426 to 1428 with at least 95% homology,subsequences of SEQ ID No. 1 to 24, 134, 168, 214, 368 to 370 SEQ ID No.530 to 553, 663, 697, 743, 897 to 899 and SEQ ID No. 1059 to 1082, 1192,1226, 1272, 1426 to 1428 and subsequences of homologues of SEQ ID No. 1to 24, 134, 168, 214, 368 to 370 SEQ ID No. 530 to 553, 663, 697, 743,897 to 899 and SEQ ID No. 1059 to 1082, 1192, 1226, 1272, 1426 to 1428with at least 95% homology.

Another embodiment relates to methods for identifying markers for thesubgroup of SLE patients with the complication lupus nephritis,comprising the comparison of the autoantibody profiles of SLE patients‘with lupus nephritis with those of SLE patients without lupusnephritis. Markers which are found by means of this embodiment of themethod are specified for example in Table 2, in group 2 and group 5.These are methods for example in which the markers for the subgroup ofthe SLE patients with the complication lupus nephritis are selected fromthe sequences

SEQ ID No. 25 to 54, 215, 216, 211, 218, 228, 233, 241, 245, 247, 249,258, 288, 289, 301, 309, 315, 316, 324, 330, 331, 337, 339, 348, 350,359, 362, 363,

SEQ ID No. 554 to 583, 744, 745, 746, 747, 757, 762, 770, 774, 776, 778,787, 817, 818, 830, 838, 844, 845, 853, 859, 860, 366, 868, 877, 879,888, 891, 892 and

SEQ ID No. 1083 to 1112, 1273, 1274, 1275, 1276, 1286, 1291, 1299, 1303,1305, 1307, 1316, 1346, 1347, 1359, 1367, 1373, 1374, 1382, 1388, 1389,1395, 1397, 1406, 1408, 1417, 1420, 1421,

homologues of SEQ ID No. SEQ ID No. 25 to 54, 215, 216, 217, 218, 228,233, 241, 245, 247, 249, 258, 288, 289, 301, 309, 315, 316, 324, 330,331, 337, 339, 348, 350, 359, 362, 363, SEQ ID No. 554 to 583, 744, 745,746, 747, 757, 762, 770, 774, 776, 778, 787, 817, 818, 830, 838, 844,845, 853, 859, 860, 866, 868, 877, 879, 888, 891, 892 and SEQ ID No.1083 to 1112, 1273, 1274, 1275, 1276, 1286, 1291, 1299, 1303, 1305,1307, 1316, 1346, 1347, 1359, 1367, 1373, 1374, 1382, 1388, 1389, 1395,1397, 1406, 1408, 1417, 1420, 1421 with at least 95% homology,subsequences of SEQ ID No. 25 to 54, 215, 216, 217, 218, 228, 233, 241,245, 247, 249, 258, 288, 289, 301, 309, 315, 316, 324, 330, 331, 337,339, 348, 350, 359, 362, 363, SEQ ID No. 554 to 583, 744, 745, 746, 747,757, 762, 770, 774, 776, 778, 787, 817, 818, 830, 838, 844, 845, 853,859, 860, 866, 868, 877, 879, 888, 891, 892 and SEQ ID No. 1083 to 1112,1273, 1274, 1275, 1276, 1286, 1291, 1299, 1303, 1305, 1307, 1316, 1346,1347, 1359, 1367, 1373, 1374, 1382, 1388, 1389, 1395, 1397, 1406, 1408,1417, 1420, 1421 and subsequences of homologues of SEQ ID No. SEQ ID No.25 to 54, 215, 216, 217, 218, 228, 233, 241, 245, 247, 249, 258, 288,289, 301, 309, 315, 316, 324, 330, 331, 337, 339, 348, 350, 359, 362,363, SEQ ID No. 554 to 533, 744, 745, 746, 747, 757, 762, 770, 774, 776778, 787, 817, 813, 830, 833, 844, 845, 353, 859, 860, 866, 868, 877,879, 888, 891, 892 and SEQ ID No. 1083 to 1112, 1273, 1274, 1275, 1276,1286, 1291, 1299, 1303, 1305, 1307, 1316, 1346, 1347, 1359, 1367, 1373,1374, 1382, 1388, 1389, 1395 1397, 1406, 1408, 1417, 1420, 1421 with atleast 95% homology.

A further embodiment relates to methods which comprise the statisticalevaluation by means of an L1-penalised logistic regression model withfive-fold cross validation and twenty times repetition and selection ofthe markers which occur at a frequency of 50% or more. Markers which canbe identified by means of this embodiment of the method are specifiedfor example in Table 2, group 2. These are methods for example in—whichthe markers for the subgroup of the SLE patients with the complicationlupus nephritis are selected from the sequences SEQ ID ho. 25 to 54, SEQID No. 554 to 583 and SEQ ID No. 1083 to 1112,

homologues of 25 to 54, SEQ ID No. 554 to 583 and SEQ ID No. 1083 to1112 with at least 95% homology, subsequences of SEQ ID No. 25 to 54,SEQ ID No. 554 to 583 and SEQ ID No. 1083 to 1112 and subsequences ofhomologues of SEQ ID No. 225 to 54, SEQ ID No. 554 to 583 and SEQ ID No.1083 to 1112 with at least 95% homology.

In a further embodiment of the method, markers for defined subgroups ofSLE patients are identified in that the sequences SEQ ID No. 1 to 529(clone sequences) are correlated with one of the sequences SEQ ID No. 1to 529 by calculation of the Spearman's rank correlation coefficient forthe particular marker. In this way, the markers of groups 1, 2 and 3 inTable 2 can be identified with the method according to the invention,for example. These are methods for example in which the markers whichdemonstrate a correlation with one another of the reactivities in SLEpatients are selected from the sequences (group 3)

SEQ ID No. 55 to 111, SEQ ID No. 584 to 1007 and SEQ ID No. 1113 to1169,

homologues of SEQ ID No. 55 to 111, SEQ ID No. 584 to 1007 and SEQ IDNo. 1113 to 1169 with at least 95% homology, subsequences of SEQ ID SEQID No. 55 to 111, SEQ ID No. 584 to 1007 and SEQ ID No. 1113 to 1169 andsubsequences of homologues of SEQ ID No. 55 to 111, SEQ ID No. 584 to1007 and SEQ ID No. 1113 to 1169 with at least 95% homology and from thesequences (group 2)

SEQ ID No. 25 to 54, SEQ ID No. 554 to 583 and SEQ ID No. 1083 to 1112,

homologues of SEQ ID No. 25 to 54, SEQ ID No. 554 to 583 and SEQ ID No.1083 to 1112 with at least 95% homology, subsequences of SEQ ID No. 25to 54, SEQ ID No. 554 to 583 and SEQ ID No. 1083 to 1112 andsubsequences of homologues of SEQ ID No. 25 to 54, SEQ ID No. 554 to 533and SEQ ID No. 1083 to 1112 with at least 95% homology and from thesequences (group 1)

SEQ ID No. 1 to 24, 134, 168, 214, 368 to 370 SEQ ID No. 530 to 553,663, 697, 743, 897 to 899 and SEQ ID No. 1059 to 1082, 1192, 1226, 1272,1426 to 1428,

homologues of SEQ ID No. 1 to 24, 134, 168, 214, 368 to 370 SEQ ID No.530 to 553, 663, 697, 743, 897 to 899 and SEQ ID No. 1059 to 1082, 1192,1226, 1272, 1426 to 1428 with at least 95% homology, subsequences of SEQID No. 1 to 24, 134, 168, 214, 368 to 370 SEQ ID No. 530 to 553, 663,697, 743, 897 to 899 and SEQ ID No. 1059 to 1082, 1192, 1226, 1272, 1426to 1428 and subsequences of homologues of SEQ ID No. 1 to 24, 134, 168,214, 368 to 370 SEQ ID No. 530 to 553, 663, 697, 743, 897 to 899 and SEQID No. 1059 to 1082, 1192, 1226, 1272, 1426 to 1428 with at least 95%homology.

One embodiment of the invention relates to methods for identifyingmarkers for the subgroup of ENA-4-negative SLE, patients. Thisembodiment of the method fox’ example comprises the testing of the serumsamples of SLE patients for the absence of autoantibodies against theextractable nuclear antigens Sm-protein, U1-RNP, Rho52/SS-A andRo60/SS-B. By way of example, the markers of group 4, Table 2 can thusbe identified. These are methods for example in which, the markers forENA-4-negative SLE patients are selected from the; sequences (group 4)

SEQ ID No. 112 to 214 and 279, SEQ ID No. 641 to 743 and 808 and SEQ IDNo. 1170 to 1272 and 1337,

homologues of SEQ ID No. 112 to 214 and 279, SEQ ID No. 641 to 743 and808 and SEQ ID No. 1170 to 1272 and 1337 with at least 95% homology,subsequences of SEQ ID No. 112 to 214 and 279, SEQ ID No. 641 to 743 and808 and SEQ ID No. 1170 to 1272 and 1337 and subsequences of homologuesof SEQ ID No. 112 to 214 and 279, SEQ ID No. 641 to 743 and 808 and SEQID No. 1170 to 1272 and 1337 with at least 95% homology.

One embodiment of the invention relates to methods comprising theselection of markers which have an adjusted p-value for thenon-parametric mean value comparison between groups of less than 0.05,and at the same time a fold change of greater than 1.5 and an AUCresulting from, the ROC analysis of greater than 0.75. By way ofexample, the markers of groups 1, 4 and 6 can thus be identified. Thecorresponding calculations for panels of markers are specified in Table5, in which the corresponding marker composition in the panels(arrangements) can be inferred from Table 4. These are methods forexample in which the markers are selected from the sequences (group 6)

SEQ ID No. 219 to 227, 229 to 232, 234 to 240, 242, 243, 244, 246, 248,250 to 257, 259 to 278, 280 to 287, 290 to 300, 302 to 308, 310 to 314,317 to 323, 325 to 329, 332 to 336, 338, 340 to 347, 349, 351 to 358,360, 361, 364 to 367,

SEQ ID No. 748 to 756, 758 to 761, 763 to 769, 771, 772, 773, 775, 777,779 to 786, 788 to 807, 809 to 816, 819 to 829, 831 to 837, 839 to 843,846 to 852, 853 to 857, 861 to 865, 867, 869 to 876, 878, 880 to 887,889, 890, 893 to 896 and

SEQ ID No. 1277 to 1285, 1287 to 1290, 1292 to 1298, 1300, 1301, 1302,1304, 1306, 1308 to 1315, 1317 to 1336, 1338 to 1345, 1348 to 1358, 1360to 1366, 1368 to 1372, 1375 to 1381, 1382 to 1386, 1390 to 1394, 1396,1398 to 1405, 1407, 1409 to 1416, 1418, 1420, 1422 to 1425,

homologues of SEQ ID No. 219 to 227, 229 to 232, 234 to 240, 242, 243,244, 246, 248, 250 to 257, 259 to 278, 280 to 287, 290 to 300, 302 to308, 310 to 314, 317 to 323, 325 to 329, 332 to 336, 338, 340 to 347,349, 351 to 358, 360, 361, 364 to 367, SEQ ID No. 748 to 756, 758 to761, 763 to 769, 771, 772, 773, 775, 777, 779 to 786, 788 to 807, 809 to816, 819 to 829, 831 to 837, 839 to 843, 846 to 852, 853 to 857, 861 to865, 867, 869 to 876, 878, 880 to 887, 889, 890, 893 to 896, SEQ ID No.1277 to 1285, 1287 to 1290, 1292 to 1298, 1300, 1301, 1302, 1304, 1306,1308 to 1315, 1317 to 1336, 1338 to 1345, 1348 to 1358, 1360 to 1366,1368 to 1372, 1375 to 1381, 1382 to 1386, 1390 to 1394, 1396, 1398 to1405, 1407, 1409 to 1416, 1418, 1420, 1422 to 1425 with at least 95%homology, subsequences of SEQ ID No. 219 to 227, 229 to 232, 234 to 240,242, 243, 244, 246, 248, 250 to 257, 259 to 278, 280 to 287, 290 to 300,302 to 308, 310 to 314, 317 to 323, 325 to 329, 332 to 336, 338, 340 to347, 349, 351 to 358, 360, 361, 364 to 367, SEQ ID No. 748 to 756, 758to 761, 763 to 769, 771, 772, 773, 775, 777, 779 to 786, 788 to 807, 809to 816, 819 to 829, 831 to 837, 839 to 843, 846 to 852, 853 to 857, 861to 865, 867, 869 to 876, 878, 880 to 887, 889, 890, 893 to 896, SEQ IDNo. 1277 to 1285, 1287 to 1290, 1292 to 1298, 1300, 1301, 1302, 1304,1306, 1308 to 1315, 1317 to 1336, 1338 to 1345, 1348 to 1358, 1360 to1366, 1368 to 1372, 1375 to 1381, 1382 to 1386, 1390 to 1394, 1396, 1398to 1405, 1407, 1409 to 1416, 1418, 1420, 1422 to 1425 and subsequencesof homologues of SEQ ID No. 219 to 227, 229 to 232, 234 to 240, 242,243, 244, 246, 248, 250 to 257, 259 to 278, 280 to 287, 290 to 300, 302to 308, 310 to 314, 317 to 323, 325 to 329, 332 to 336, 338, 340 to 347,349, 351 to 358, 360, 361, 364 to 367, SEQ ID No. 748 to 755, 753 to761, 763 to 769, 771, 772, 773, 775, 777, 779 to 786, 788 to 807, 809 to816, 819 to 829, 831 to 837, 839 to 843, 846 to 852, 853 to 857, 861 to865, 867, 369 to 876, 878, 880 to 887, 889, 890, 893 to 896, SEQ ID No.1277 to 1285, 1287 to 1290, 1292 to 1238, 1300, 1301, 1302, 1304, 1306,1308 to 1315, 1317 to 1336, 1338 to 1345, 1348 to 1358, 1360 to 1366,1368 to 1372, 1375 to 1381, 1382 to 1386, 1390 to 1394, 1396, 1398 to1405, 1407, 1409 to 1416, 1418, 1420, 1422 to 1425 with at least 95%homology.

Group 7 in table 2 contains a further 85 statistically significantantigens from the methods according to the invention; these are markersselected from the sequences SEQ ID No. 368 to 452, SEQ ID No. 897 to981, SEQ ID No. 1426 to 1510, homologues of SEQ ID No. 368 to 452, SEQID No. 897 to 981, SEQ ID No. 1426 to 1510 with at least 95% homology,subsequences of SEQ ID No. 368 to 452, SEQ ID No. 897 to 981, SEQ ID No.1426 to 1510 and subsequences of homologues of SEQ ID No. 368 to 452,SEQ ID No. 897 to 981, SEQ ID No. 1426 to 1510 with at least. 95%homology, which can be used for the diagnosis and differential diagnosisof SLE compared with healthy individuals and other autoimmune diseases.Antigens from group 7 were also used for the calculation of biomarkercombinations.

Group 8 consists of further statistically significant antigens from themethods according to the invention; markers selected from the sequencesSEQ ID No. 453 to 529, SEQ ID No. 982 to 1058, SEQ ID No. 1511 to 1587,homologues of SEQ ID No. 453 to 529, SEQ ID No. 982 to 1058, SEQ ID No.1511 to 1587 with at least 95% homology, subsequences of SEQ ID No. 453to 529, SEQ ID No. 982 to 1058, SEQ ID No. 1511 to 1587 and subsequencesof homologues of SEQ ID No. 453 to 529, SEQ ID No. 982 to 1058, SEQ IDNo. 1511 to 1587 with at least 95% homology were detected and identifiedfor the autoantibodies in SLE patients.

The invention also relates to the individual markers for SLE identifiedwith the method according to the invention. The method concerns markersfor SLE selected from the sequences SEQ ID No. 1 to 1587, homologues ofsequences SEQ ID No. 1 to 1587 with at least 95% homology, subsequencesof SEQ ID No. 1 to 1587 and subsequences of homologues of SEQ ID No. 1to 1587 with at least 95% homology. The method concerns the markers ofgroups 1, 2, 3, 4, 5, 6, 7, 8 in Table 2, wherein, the respective groupscomprise the markers of the clone sequences specified in Table 2, thecorresponding RNA sequences, the corresponding protein, sequences, therelevant homologues with a homology of at least 95%, and the relevantsubsequences. The invention relates to a marker for SLE selected fromthe sequences SEQ ID No. 530 to 1058 (RNA sequences), SEQ ID No. 1059 to1587 (protein sequences). The markers according to the invention and theassociated nucleic acid sequences are presented in Table 2 (SEQ ID No.of the relevant clone sequences is specified) and can be unambiguouslyidentified by their cited database entry, for example athttp;//www.ncbi.nlm.nih, gov/, by means of their Gene ID (Table 2). Thesequences SEQ ID No. 1-1587 are specified in the accompanying sequenceprotocol, wherein SEQ ID No. 1-529 are clone sequences (cDNA), SEQ IDNo. 530-1058 are RNA sequences, and SEQ ID No. 1059-1587 are proteinsequences.

The invention also relates to the proteins coded, by sequences SEQ IDNo. 1 to 1058, the proteins coded by homologues of the sequences SEQ IDNo. 1 to 1058 with at least 95% homology to the sequences SEQ ID No. 1to 1058, the proteins coded by subsequences of SEQ ID No. 1 to 1058, theproteins coded by homologues of the subsequences of SEQ ID No. 1 to 1058with at least 95% homology in. the subsequences. In a preferredembodiment these are the proteins SEQ ID No. 1059 to 1587, homologues ofthe proteins with the sequences SEQ ID No. SEQ ID No. 1059 to 1587 withat least 95% homology, subsequences of SEQ ID No. 1059 to 1587,homologues of the subsequences of SEQ ID No. SEQ ID No. 1059 to 1587with at least 95% homology.

The invention also relates to a panel of markers (also referred to as anarrangement of markers), comprising at least two different markers forSLE which are selected independently of one another from the sequencesSEQ ID No. 1 to 1587, homologues of sequences SEQ ID No. 1 to 1587 withat least 95% homology, subsequences of SEQ ID No. 1 to 1587 andsubsequences of homologues of SEQ ID No. 1 to 1587 with, at least 95%homology. A panel of markers for SLE can comprise 2 to 20 or more, forexample 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,25, 30, 40, 50, 100 or more different markers for SLE and optionallyfurther markers, wherein the markers of SLE are selected independentlyof one another from the sequences SEQ ID No. 1 to 1587, homologues ofsequences SEQ ID No. 1 to 1587 with at least 95% homology, subsequencesof SEQ ID No. 1 to 1587 and subsequences of homologues of SEQ ID No. 1to 1587 with at least 95% homology, and the proteins coded by thesequences.

On account of the high clinical and serological heterogeneity of the SLEdisease, it is difficult, to diagnose SLE unambiguously using just onebiomarker. It is therefore often necessary to combine (where possible)uncorrelated autoantigens to form what are known as panels of markers(biomarker panels for SLE). By way of example, within the scope ofindividualised medicine, corresponding panels of markers for SLE can becomposed individually for the relevant SLE subtype (subgroup) forindividual patients or patient groups. It is therefore also necessary tohave available a multiplicity of potential markers for SLE in order toselect, suitable subgroups or subtypes of pecific markers for SLE forthe individual case in question. A orresponding panel can be embodiedfor example in the form of an arrangement, an array, or also one or morebeads, preferably Luminex beads. The invention thus relates to anarrangement comprising one or more markers according to the invention, aprotein array comprising one or more markers according to the invention,a bead (small ball or platelet) comprising one or more markers accordingto the invention. Examples of SLE panels (SLE arrangements) are given inTable 4.

The invention also relates to a diagnostic device or a test kitcomprising at least one marker for SLE selected from the sequences SEQID No. 1 to 1587, homologues of sequences SEQ ID No. 1 to 1587 with atleast 95% homology, subsequences of SEQ ID No. 1 to 1587 andsubsequences of homologues of SEQ ID No. 1 to 1587 with at least 95%homology, and the proteins coded by the sequences. A correspondingdiagnostic device or a corresponding test kit can also comprise a panelof markers for SLE and optionally further auxiliaries and additives.

The invention also relates to the use of one or more markers for SLEselected from sequences SEQ ID No. 1 to 1587, homologues of sequencesSEQ ID No. 1 to 1587 with at least 95% homology, subsequences of SEQ IDNo. 1 to 1587 and subsequences of homologues of SEQ ID No. 1 to 1587with at least 95% homology, and the proteins coded by the sequences, amarker panel for SLE, or a diagnostic device or test kit for identifyingsubgroups of SLE patients, for diagnosing SLE, for differentialdiagnosis (i.e. for distinction from other autoimmune diseases or otherrheumatic diseases), for prognosis in the case of SLE, for therapycontrol in the case of SLE, for active substance selection in the caseof SLE, for therapy monitoring in the case of SLE, or for aftercare inthe case of SLE.

The invention also relates to the use of one or more of the markers forSLE selected from the sequences SEQ ID No. 1 to 1587, homologues ofsequences SEQ ID No. 1 to 1587 with at least 95% homology, subsequencesof SEQ ID No. 1 to 1587 and subsequences of homologues of SEQ ID No. 1to 1587 with at least 95% homology, and the proteins coded by thesequences for the differentiation of SLE from RA and/or other autoimmunediseases, for example SSc and/or SPA and/or RA and/or early RA.

The Invention also relates to the use of one or more markers for SLEselected from the sequences SEQ ID No. 112 to 214 and 279, SEQ ID No.641 to 743 and 808 and SEQ ID No. 1170 to 1272 and 1337, homologues ofSEQ ID No. 112 to 211 and 279, SEQ ID No. 641 to 743 and 808 and SEQ IDNo. 1170 to 127.2 and 1337 with at least 95% homology, subsequences ofSEQ ID No. 112 to 214 and 279, SEQ ID No. 641 to 743 and 808 and SEQ IDNo. 1170 to 1272 and 1337 and subsequences of homologues of SEQ ID No.112 to 214 and 279, SEQ ID No. 641 to 743 and 808 and SEQ ID No. 1170 to1272 and 1337 with at least 95% homology, and the proteins coded by thesequences for the diagnosis of SLE in ENA-4-negative SLE patients.

The invention also relates to the use of one or more markers for SLEselected from the sequences SEQ ID No. 25 to 54, SEQ ID No. 554 to 583and SEQ ID No. 1083 to 1112, homologues of SEQ ID No. 25 to 54, SEQ IDNo. 554 to 583 and SEQ ID No. 1083 to 1112 with at least 95% homology,subsequences of SEQ ID No. 25 to 54, SEQ ID No. 554 to 583 and SEQ IDNo. 1083 to 1112 and subsequences of homologues of SEQ ID No. 25 to 54,SEQ ID No. 554 to 583 and SEQ ID No. 1083 to 1112 with at least 95%homology, and the proteins coded by the sequences for the diagnosis anddifferential diagnosis of lupus nephritis in SLE patients. Lupusnephritis is a common and serious complication of SLE. In the case ofcomplete failure of the kidney function, therapy with dialysis isnecessary. In order to avoid long-term damage, it is therefore importantto identify and treat any kidney involvement early on. This is also ofparticular importance for the development of active substances for SLEin general, i.e. for the development of active substances for patientswith lupus nephritis. Previously, there were still no biomarkersavailable able to diagnose lupus nephritis in all patients.

The invention also relates to markers for SLE and lupus nephritisselected from the sequences SEQ ID No. 25 to 54, SEQ ID No. 554 to 583and SEQ ID No. 1083 to 1112, homologues of SEQ ID No. 25 to 54, SEQ IDNo. 554 to 583 and SEQ ID No. 1083 to 1112 with at least 95% homology,subsequences of SEQ ID No. 25 to 54, SEQ ID No. 554 to 583 and SEQ IDNo. 1083 to 1112 and subsequences of homologues of SEQ ID No. 25 to 54,SEQ ID No. 554 to 583 and SEQ ID No. 1083 to 1112 with at least S5%homology, and the proteins coded by the sequences.

The autoantibody profiles of SLE patients with lupus nephritis weretherefore compared with those without lupus nephritis. Followingunivariate statistical evaluation, a threshold value of p<0.05 and a 1.5times modified reactivity compared with the control group were applied.

The invention also relates to a method for the early detection,diagnosis, differential diagnosis, prognosis, therapy control and/orafter-care of SLE, in which

-   a. at least one of the markers for SLE selected from the sequences    SEQ ID No. 1 to 1587, the homologues of sequences SEQ ID No. 1 to    1587 with at least S5% homology, the subsequences of SEQ ID No. 1 to    1587 or the subsequences of homologues of SEQ ID No. I to 1587 with    at least 95% homology, and the proteins coded by the sequences-   b. is brought into contact with bodily fluid or a tissue sample from    an individual to be tested, and-   c. an interaction of the bodily fluid or of the tissue sample with    the one this or more markers from a, is detected.

The invention also relates to a target tor the therapy of SLE selectedfrom the sequences SEQ ID No. 1 to 1587, the homologues of sequences SEQID No. 1 to 1587 with at least 95% homology, the subsequences of SEQ IDNo. 1 to 1587 and the subsequences of homologues of SEQ ID No. 1 to 1587with at least 95% homology, and the proteins coded by the sequences.

The invention also relates to a composition, in particular apharmaceutical composition, comprising at least one of the sequences SEQID No. 1 to 1587, the homologues of sequences SEQ ID No. 1 to 1587 withat least 95% homology, the subsequences of SEQ ID No. 1 to 1587 or thesubsequences of the homologues of SEQ ID No. 3. to 1587 with at least95% homology, and the proteins coded, by the sequences.

The invention also relates to a method for screening active substancesfor SLE, in which

-   a. at least cone of the markers for SLE selected from the sequences    SEQ ID No. 1 to 1587, the homologues of sequences SEQ ID No. 1 to    1587 with at least 95% homology, the subsequences of SEQ ID No. 1 to    1587 or the subsequences of homologues of SEQ ID No. 1 to 1587 with    at least 95% homology, and the proteins coded by the sequences-   b. is brought into contact with a substance to be tested, and-   c. an interaction of the substance with the one or more markers    from a. is detected.

The large clinical heterogeneity of SLE currently constitutes a bigproblem both for diagnosis and for active substance development.

The identification of specific antibody signatures in SLE patientsubgroups therefore constitutes an important step for the improveddefinition of patient groups in clinical studies. By way of example, aspresented under Example 9, specific autoantibodies for lupus nephritiscould be used to recruit this subgroup for drug studies.

A large number of new active substances and therapeutic antibodies arecurrently undergoing clinical development: inter alia, therapeuticantibodies against cell-surface receptors of immune cells, such asanti-CD20, anti-CD22, or against pro-inflammatory cytokines, such asanti-IL6, are being developed, It is therefore now possible, due to theidentification of serologically defined subgroups of SLE, to link thisto a target-specific response to a drug.

The invention also relates to the use of one or more markers for SLEaccording to the invention, of an arrangement according to the invention(panel of markers for SLE), of a protein array according to theinvention, of a bead according to the invention, of a diagnostic deviceaccording to the invention, or of a. test kit according to the inventionfor the individualised diagnosis and/or therapy in individual patients,patient groups, cohorts, population groups, variants of SLE, or stagesof SLE.

The invention also relates to the use of one or more markers accordingto the invention for SLE, of an arrangement according to the invention(panel of markers for SLE), of a protein array according to theinvention, of a bead according to the invention, of a diagnostic deviceaccording to the invention, or of a test kit according to the inventionfor the detection and/or determination of the amount of one or moreautoantibodies associated with SLE, for example in bodily fluids such asserum, tissue or tissue samples of the patient. The invention alsorelates to the use of one or more markers according to the invention, ofan arrangement according to the invention, of a protein array accordingto the invention, of a bead according to the invention, of a diagnosticdevice according to the invention, or of a test kit according to theinvention for the analysis of autoantibody profiles of patients, inparticular for the qualitative and/or quantitative analysis ofautoantibodies and/or for the monitoring of changes of autoantibodyprofiles associated with SLE, for example in bodily fluids such asserum, tissue or tissue samples of the patient.

A particular embodiment of the invention relates to methods for theearly identification and diagnosis of SLE, in which the detection of aninteraction of the bodily fluid or the tissue sample with the one ormore markers indicates an SLE-associated autoantibody profile of thepatient or of a cohort or of a population group or of a certain courseof disease (prognosis) or of a certain response to a therapy/drug.

The invention therefore includes the use of at least one marker for SLEselected from the sequences SEQ ID No. 1 to 1587, the homologues ofsequences SEQ ID No. 1 to 1587 with at least 95% homology, thesubsequences of SEQ ID No. 1 to 1587 or the subsequences of homologuesof SEQ ID No. 1 to 1587 with at least 95% homology, and the proteinscoded by the sequences for the analysis of autoantibody profiles ofpatients, in particular for the quantitative analysis and/or for themonitoring of changes of autoantibody profiles of SLE patients.

An interaction of the bodily fluid or the tissue sample with the one ormore SLE markers can be detected for example by a probe, in particularby an antibody.

In a preferred embodiment at least 2, for example 3, 4, 5, 6, 7, 8, 9,10, preferably 15 to 20 markers for SLE or 30 to 50 or 100 or moremarkers are used together or in combination, either simultaneously or insuccession, wherein the markers for SLE are selected independently ofone another from the sequences SEQ ID No. 1 to 1587, the homologues ofsequences SEQ ID No. 1 to 1587 with at least 95% homology, thesubsequences of SEQ ID No. 1 to 1587 or the subsequences of homologuesof SEQ ID No. 1 to 1587 with at least 95% homology, and the proteinscoded by the sequences.

A particular embodiment of the invention relates to a method accordingto the invention, wherein the stratification or therapy control includesdecisions relating to the treatment and therapy of the patient, inparticular hospitalisation of the patient, use, efficacy and/or dosageof one or more drugs, a therapeutic measure, or the monitoring of thecourse of the disease and course of therapy, aetiology, orclassification of a disease inclusive of prognosis. The invention alsorelates to a. method for stratification, in particular for riskstratification and/or therapy control of a patient with SLE.

The stratification of the patient with SLE into new or established SLEsubgroups as well as the expedient selection of patient croups for theclinical development of new therapeutic agents is also included. Theterm therapy control likewise includes the division of patients intoresponders and non-responders with regard to a therapy or coursethereof.

The invention in particular also relates to the detection anddetermination of the amount of at least two different autoantibodies ina patient by means of the SLE markers according to the invention,wherein at least two different SLE markers are preferably used. Theinvention also relates to a use according to the invention of one ormore SLE markers, wherein at least 2, for example 3 to 5 or 10,preferably 30 to 50, or 50 to 100 or more SLE markers or the relevantautoantibodies on or from a patient to be tested are determined.

The invention comprises the SLE markers on a solid substrate, forexample a filter, a membrane, a small platelet or ball, for example amagnetic or fluorophore-labelled ball, a silicon wafer, a bead, a chip,a mass spectrometry target, or a matrix, or the like. Differentmaterials are suitable as substrates and are known to a person skilledin the art, for example glass, metal, plastic, filter, PVDF,nitrocellulose, or nylon (for example Immobilon P Millipore, ProtranWhatman, Hybond N+Amersham).

The substrate tor example can correspond to a grid with the dimensionsof a microtitre plate (8-12 well strips, 96 wells, 384 wells or more),of a silicon wafer, of a chip, of a mass spectrometry target, or of amatrix.

In one embodiment of the invention markers for SLE are present in theform of clone sequences or clone(s).

The markers according to the invention can be combined, supplemented orextended with known biomarkers for SLE or biomarkers for other diseases.With a combination of this type, a proportion of markers for SLEaccording to the invention of preferably at least 50%, preferably 60%,and particularly preferably 70% or more is comprised.

In a preferred embodiment the use of the SLE markers and the methodsaccording to the invention are implemented outside the human or animalbody, for example the diagnosis is performed ex vivo/in vitro,preferably by means of an assay, as detailed below,

In the sense of this invention, the term “diagnosis” means the positivedetermination of SLE with the aid of the markers according to theinvention and the assignment of the patients or symptoms thereof to thedisease SLE. The term “diagnosis” includes the medical diagnosis andtests in this respect, in particular in vitro diagnosis and laboratorydiagnosis, and also proteomics and nucleic acid blots. Further tests maybe necessary for assurance and in order to rule out other diseases. Theterm “diagnosis” therefore includes in particular the differentialdiagnosis of SLE by means of the markers according to the invention.

In the sense of this invention, “stratification or therapy control”means that, for example, the methods according to the invention allowdecisions for the treatment and therapy of the patient, whether it isthe hospitalisation of the patient, the use, efficacy and/or dosage ofone or more drugs, a therapeutic measure or the monitoring of the courseof a disease and the course of therapy or aetiology or classification ofa disease, for example into a new or existing sub-type, or thedifferentiation of diseases and patients thereof. In a furtherembodiment of the invention, the term “stratification” in particularincludes the risk, stratification with the prognosis of an “outcome” ofa negative health event,

“Prognosis” means the prediction of the course of a disease.

In accordance with the invention, “therapy control” means, for example,the prediction and monitoring of the response to a drug or a therapy as‘well as aftercare.

Within the scope of this invention, the term “patient” is understood tomean any test subject, any individual (human or mammal), with theprovision that the test subject or individual is tested for SLE.

The term “marker for SLE” in the sense of this invention means that thenucleic acid, for example DNA, in particular cDNA or RNA or the codedamino acid sequence or the polypeptide or protein are significant(specific) for SLE and/or the autoantibody profiles associated with SLE,Markers according to the invention are nucleic acid sequences and/oramino acid sequences according to the definition in the appendedsequence protocol (SEQ ID No. 1 to SEQ ID No. 1587), homologues andsubsequences thereof, wherein modified nucleic acid and amino acidsequences are also included. Here, marker’ for SLE means, for example,that the cDNA or RNA or the polypeptide or protein obtainable therefrominteracts with substances from the bodily fluid or tissue sample from apatient with SLE (for example antigen (epitope)/antibody (paratope)interaction). In a particularly preferred, embodiment of the inventionthe marker for SLE is an antigen or part of an antigen or codes for anantigen or for part of an antigen.

The substances from the bodily fluid or tissue sample occur either onlyin an amplified manner or at least in an amplified manner in the case ofSLE or are expressed, whereas these substances are not present inpatients without SLE or healthy individuals, or at least are present toa lesser extent (smaller amount, lower concentration). Markers for SLEcan also be characterised in that they interact with substances from thebodily fluid or tissue sample from patients with SLE, because thesesubstances no longer occur or are no longer expressed or occur or areexpressed at least in a much lower amount/concentration in the case ofSLE, whereas these substances are present or are at least present to amuch higher extent in patients without SLE. Markers for SLE can also bepresent in healthy test subjects, however the amount (concentration)thereof changes for example with the development, establishment andtherapy of SLE. One or more markers can in this way map a profile ofsubstances from bodily fluid and tissue sample, for example anSLE-asscciated autoantibody profile of the patient in question. Markersaccording to the invention are biomarkers for SLE.

Autoantibody profiles comprise the amount of one or more autoantibodiesof which the occurrence/expression accompanies the development and/orestablishment of SLE, Autoantibody profiles therefore include on the onehand the composition, i.e. one or more autoantibodies is/are expressedonly in the case of SLE for example, and also the amount/concentrationof individual autoantibodies, i.e. the amount/concentration ofindividual autoantibodies changes with the development and establishmentof SLE. These changes can be detected with the aid of the markersequences according to the invention.

In a particularly preferred embodiment the SLE marker identifies/bindsto autoantibodies which are present (intensified) or are present to alower extent (or no longer) during the course of the development,establishment and therapy of SLE. Autoantibodies are formed by the bodyagainst, endogenous antigens which are formed for example in the case ofSLE, Autoantibodies are formed by the body against different substancesand pathogens, Within the scope of the present invention, theautoantibodies which are formed with the occurrence and during thecourse of the development of SLE and/or of which the expression isup-regulated or down-regulated are detected in particular. Theseautoantibodies can be detected with the aid of the methods and markersaccording to the invention, and the detection and monitoring (forexample of the amount) thereof can be used for the early identification,diagnosis and/or therapy monitoring/therapy control and the prognosisand prediction of the risk of the re-occurrence of SLE within the scopeof the after-care.

The autoantibody profiles can be sufficiently characterized with use ofjust a single SLE marker. In other cases, two or more SLE markers arenecessary in order to map an autoantibody profile which is specific forSLE.

In one embodiment of the invention autoantibodies ‘which derive fromanother individual and which for example originate from a commercialcDNA bank can be detected using SLE markers.

In another embodiment of the invention these autoantibodies can bedetected using SLE markers ‘which derive from the same individual andwhich for example originate from a cDNA bank produced individually forthe patient or a group of patients for example within the scope ofindividualised medicine, By way of example, homologues of the specifiedSLE markers with the sequences SEQ ID. No. 1 to 1587 or subsequencesthereof can be used.

Autoantibodies can be formed by the patient already many years prior tothe occurrence of the first symptoms of disease. An earlyidentification, diagnosis and also prognosis and preventative treatmentor lifestyle change and other possibilities for prevention mighttherefore be possible even years prior to the visible outbreak of thedisease. The devices, means and methods according to the inventionenable a very early intervention compared with known methods, whichsignificantly improves the prevention, treatment possibilities andeffects of SLE.

Since the SLE-associated autoantibody profiles change daring theestablishment and treatment/therapy of SLE, the invention also enablesthe detection and monitoring of SLE at any stage of the development andtreatment and also monitoring within the scope of SLE after-care. Themeans according to the invention, for example a corresponding diagnosticdevice or a test kit, also allow simple handling at home by the patientand an economical routine precautionary measure for earlyidentification.

In particular due to the use of antigens as specific markers for SLEwhich derive from sequences already known, for example from commercialcDNA banks, test subjects can be tested and any present SLE-associatedautoantibodies can be detected in these test subjects, even if thecorresponding autoantigens are not (yet) known in these test subjects.

Different patients can have different SLE-associated autoantibodyprofiles, for example different cohorts or population groups can differfrom one another. Here, any patient can form one or more differentSLE-associated autoantibodies during the course of the development ofSLE and the progression of the SLE disease, that is to say evendifferent autoantibody profiles. In addition, the composition and/or theamount of formed autoantibodies can change during the course of the SLEdevelopment and progression of the disease, such that a quantitativeevaluation is necessary. The therapy/treatment, of SLE leads to changesin the composition and/or the amount of SLE-associated autoantibodies.The large selection of SLE markers according to the invention which areprovided with this invention enables the individual compilation of SLEmarkers in an arrangement, i.e. a panel, for individual patients, groupsof patients, certain cohorts, population groups and the like. In oneindividual case, the use of one SLE marker may therefore be sufficient,‘whereas in other cases at least two or more SLE markers must be used,together or in combination in order to create a conclusive autoantibodyprofile.

Compared with other biomarkers, the detection of SLE-associatedautoantibodies for example in the serum or plasma of patients has theadvantage of high stability and storage capability and gooddetectability, The presence of autoantibodies also is not subject to acircadian rhythm, and therefore the sampling is independent of the timeof day, food intake, and the like.

In addition, the SLE-associated autoantibodies can be detected with theaid of the corresponding antigens/autoantigens in known assays, such asELISA or Western Blot, and the results can be checked in this way.

In the sense of the invention, an interaction between the SLE marker andthe serum in question, for example an autoantibody of the patient, isdetected. Such an interaction is, for example, a bond, in particular abinding substance on at least one SLE-specific marker, or, In the casethat the SLE-specific marker is a nucleic acid, for example a cDNA, thehybridization with a suitable substance under selected conditions, inparticular stringent, conditions (for example as defined conventionallyin J, Sambrook, E, F. Fritsch, T. Maniatis (1989), Molecular cloning; Alaboratory manual, 2nd Edition, Cold Spring Habor Laboratory Press, ColdSpring Habor, USA or Ausubel, “Current Protocols in Molecular Biology”,Green Publishing Associates and Wiley Interscience, N.Y. (1989)). Oneexample of stringent hybridisation conditions is: hybridization in 4×SSCsit 65° C. (alternatively in 50% formamide and 4×SSC at 42° C.),followed by a number of washing steps in 0.1×SSC at 65° C. for a totalof approximately one hour. An example of less stringent hybridisationconditions is hybridisation in 4×SSC at 37 *C, followed by a number ofwashing steps in 1×SSC at room temperature. The interaction between thebodily fluid or tissue sample from a patient and the markers for SLE ispreferably a protein-protein interaction.

In accordance with the invention, such substances, for example antigens,autoantigens and SLE-assedated autoantibodies_(f) are part of a bodilyfluid, in particular blood, whole blood, blood plasma, blood serum,patient serum, urine, cerebrospinal fluid, synovial fluid or a tissuesample from the patient. The invention in particular relates to the useof these bodily fluids and tissue samples for early detection,diagnosis, prognosis, therapy control and aftercare.

The SLE-specific markers, in a further embodiment of the invention, havea recognition signal that is addressed to the substance to be bound (forexample antibody, nucleic acid). In accordance with the invention, therecognition signal for a protein is preferably an epitope and/orparatope and/or hapten, and for a cDNA is preferably a hybridisation orbinding region.

Homologues of the markers according to the invention SEQ ID No. 1 to1587, as presented in the claims for example are also included. Withinthe sense of the invention, homologues are those with homology of theamino or nucleic acid sequence and those in which the correspondingsequence is modified, for example the protein variants, which indeedhave the same amino acid sequence, but differ with regard to themodification, in particular’ the post-translational modification.

In accordance with the invention, modifications of the nucleic acidsequence and of the amino acid sequence, for example citrullination,acetylation, phosphorylation, glycosylation, ethylation, or polyA strandextensions and further modifications known as appropriate to a personskilled in the art are included.

Homologues also include sequence homologues of the markers andsubsequences thereof. Sequence homologues are, for example, nucleic acidsequences and/or protein sequences that have an identity with the SLEmarkers of the sequences SEQ ID No. 1 to 1587 of at least 70% or 80%,preferably 90% or 95%, particularly preferably 96% or 97% or more, forexample 98% or 99%. In a particularly preferred embodiment of theinvention, for the case in which the SLE markers are antigens, thehomology in the sequence range in which the antigen-antibody orantigen-autoantibody interaction takes place, is at least 95%,preferably at least 97%, particularly preferably at least 99%, Forexample, mutations such as base exchange mutations, frameshiftmutations, base insertion mutations, base loss mutations, pointmutations and insertion mutations, are included in accordance with theinvention.

The invention also relates to subsequences of the SLE markers with thesequence SEQ ID No. 1 to 1587, Subsequences also include nucleic acid oramino acid sequences that are shortened compared with the entire nucleicacid or the entire protein/peptide. Here, the deletion may occur at theend or the ends and/or within the sequence, For example, subsequencesand/or fragments that have 50 to 100 nucleotides or 70-120 nucleotidesof the sequence SEQ ID No. 1 to 1587 are included. Homologues ofsubsequences are also included in accordance with the invention. In aparticular embodiment, the SLE markers are shortened compared with thesequences SEQ ID No. 1 to 1587 to such an extent that, they stillconsist only of the binding point(s) for the SLE-associated autoantibodyin question. In accordance with the invention, SLE markers are alsoincluded that differ from the sequences SEQ ID No. 1 to 1587 in thatthey contain one or more insertions, wherein the insertions for exampleare 1 to 100 or more nucleotide/amino acids long, preferably 5 to 50,particularly preferably 10 to 20 nucleotides/amino acids long and thesequences are otherwise identical however or homologous to sequences SEQID No. 1 to 1587. Subsequences that have at least 90%, preferably atleast 95%, particularly preferably 97% or 98%, of the length of the SLEmarkers according to the Invention ‘with sequences SEQ ID No. 1 to 1587are particularly preferred.

In a further embodiment, the respective SLE marker can be represented indifferent quantities in one or more regions in the arrangement, or onthe substrate or in a panel. This allows a variation of the sensitivity.The regions may each have a totality of SLE markers, that is to say asufficient number of different SLE markers, in particular 2, 3, 4, 5, 6,7, 8, 9 or 10 or more different SLE markers. By way of example, 20 to 50(numerically) or more, preferably more than 100, particularly preferably150 or more, for example 25,000 or 5000 or 10000 different or same SLEmarker sequences and where applicable further nucleic acids and/orproteins, in particular other biomarkers can be represented on thesubstrate or in the panel.

One or more panels as presented in the examples and selected from thesequences, preferably protein sequences, consisting of at least twomarkers, five markers or 10 markers or more, selected from:

panel I (PI)

SEQ ID No. 1, 2, 3, 5, 7, 8, 10, 12, 13, 15, 17, IS, 19, 20, 24,

SEQ ID No. 530, 531, 532, 534, 536, 537, 539, 541, 542, 544, 546, 547,548, 549, 553, preferably

SEQ ID No. 1059, 1060, 1061, 1063, 1065, 1066, 1068, 1070, 1071, 1073,1075, 1076, 1077, 1078, 1082, and/or

panel II (P2)

SEQ ID No. 1, 3, 4, 5, 7, 12, 13, 14, 15, 17, 18, 19, 20, 24

SEQ ID No. 530, 532, 533, 534, 536, 541, 542, 543, 544, 546, 547, 548,549, 553, preferably

SEQ ID No. 1059, 1061, 1062, 1063, 1065, 1070, 1071, 1072, 1073, 1075,1Q 7 6, 1077, 1078, 1082, and/or

panel III (P3)

SEQ ID No. 1, 2, 3, 5, 6, 7, 8, 9, 10, 15, 16, 18-21, 23

SEQ ID No. 530, 531, 532, 534, 535, 536, 537, 538, 539, 544, 545, 547,550, 552, preferably

SEQ ID No. 1059, 1060, 1061, 1063, 1064, 1065, 1066, 1067, 1068, 1073,1074, 1076, 1079, 1081, and/or

panel IV (P4)

SEQ ID No. 1, 2, 3, 4, 5, 8, 9, 10, 12, 13, 14, 15, 17, 19, 20

SEQ ID No. 530, 531, 532, 533, 534, 537, 538, 539, 541, 542, 543, 544,546, 548, 549, preferably

SEQ ID No. 1059, 1060, 1061, 1062, 1063, 1066, 1067, 1068, 1070, 1071,1072, 1073, 1075, 1077, 1078, and/or

panel V

SEQ ID No. 1, 2, 3, 4, 5, 6, 7, 1.1, 15, 16, 18, 21, 22, 23, 24

SEQ ID No. 530, 531, 532, 533, 534, 535, 53 6, 540, 54 4, 545, 547, 550,551, 552, 553, preferably

SEQ ID No. 1059, 1060, 1061, 1062, 1063, 1064, 1065, 1069, 1073, 1074,1076, 1079, 1080, 1081, 1082, and/or

panel VI

SEQ ID No. 2, 5, 6, 7, 8, 10, 13, 18, 19, 22, 168

SEQ ID No. 531, 534, 535, 536, 537, 539, 542, 547, 548, 551, 697,preferably

SEQ ID No. 1060, 1063, 1064, 1065, 1066, 1068, 1071, 1076, 1077, 1080,1226, and/or

panel VII

SEQ ID No. 1, 2, 5, 6, 7, 8, 9, 10, 13, 15, 19, 22, 24, 134, 168, 214,368, 369, 370

SEQ ID No. 530, 531, 534, 535, 536, 537, 538, 539, 542, 544, 548, 551,553, 663, 697, 743, 897, 898, 899, preferably

SEQ ID No. 1059, 1060, 1063, 1064, 1065, 1066, 1067, 1068, 1071, 1073,1077, 1080, 1082, 1192, 1226, 1272, 1426, 1427, 1428, and/or

panel VIII (P8)

SEQ ID No. 1, 2, 4, 5, 6, 7, 8, 9, 10, 12, 13, 15, 17, 18, 19, 20, 21,22, 23, 24, 29, 31, 46, 95, 128, 134, 136, 143, 163, 168, 169, 171, 188,214, 349, 368, 369, 370, 371-392, 424-434

SEQ ID No. 530, 531, 533, 534, 535, 536, 537, 538, 539, 541, 542, 544,546, 547, 548, 549, 550, 551, 552, 553, 558. 560, 575, 624, 657, 663,665, 692, 697, 698, 700, 717, 743, 878, 897, 898, 899, 900-921, 953-963,preferably

SEQ ID No, 1059, 1060, 1062, 1063, 1064, 1065, 1066, 1067, 1068, 1070,1071, 1073, 10075, 1076, 1077, 1078, 1079, 1080, 1081, 1082, 1087, 1089,1104, 1153, 1186, 1192, 1194, 1221, 1222, 1226, 1227, 1229, 1246, 1272,1407, 1426, 1427, 1428, 1429-1450, 1482-1492, and/or

panel IX (P9)

SEQ ID No. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,18, 19, 20, 21, 22, 23, 24, 29, 31, 33, 41, 46, 48, 74, 95, 105, 108,114, 115, 116, 128, 132, 134, 136, 143, 163, 168, 169, 171, 188, 214,349, 368, 369, 370, 37-39, 42-434

SEQ ID No. 530, 531, 532, 533, 534, 535, 536, 537, 538, 539, 540, 541,542, 543, 544, 545, 546, 547, 548, 549, 550, 551, 552, 553, 558, 560,562, 570 575, 577, 603, 624, 634, 637, 643, 644, 645, 657, 661, 663,6665, 672, 692, 697, 698, 700, 717, 743, 878, 897, 898, 899, 900-921,953-963, preferably

SEQ ID No. 1059, 1060, 1061, 1062, 1063, 1064, 1065, 1066, 1067, 1068,1069, 1070, 1071, 1072, 1073, 1074, 1075, 1076, 1077, 1078, 1079, 1080,1081, 1082, 1087, 1089, 1091, 1099, 1104, 1106, 1132, 1153, 1163, 1166,1172, 1173, 1174, 1186, 1190, 1192, 1194, 1201, 1221, 1226, 1227, 1229,1246, 1272, 1407, 1426, 1427, 1428, 1429-1450, 1482-1492 or respectivehomologues or subsequences thereof, as mentioned previously with regardto the individual marker sequences, is/are very particularly preferred.

These aforementioned panels particularly advantageously allow theexecution of the method according to the invention; see the examples.

Within the scope of this invention, “arrangement” is synonymous with“array”, and, if this “array” is used to identify substances on SLEmarkers, this is to be understood preferably to be an “assay” or a beador a diagnostic device or a screening assay. In a preferred embodiment,the arrangement is designed such that the markers represented on thearrangement are present in the form of a grid on a substrate.Furthermore, those arrangements are preferred that permit a high-densityarrangement of SLE markers. The markers are preferably spotted. Suchhigh-density spotted arrangements are disclosed for example in WO99/57311 and WO 99/57312 and can be used advantageously in arobot-supported automated high-throughput method.

Within the scope of this invention, however, the term “assay” ordiagnostic device likewise comprises those embodiments such as ELISA,bead-based assay, line assay, Western Blot, and immunochromatographicmethods (for example what are known as lateral flow immunoassays) orsimilar immunological single or multiplex detection methods.

A “protein array” in the sense of this invention is the systematicarrangement of SLE markers on. a solid substrate, wherein the substratecan have any shape and/or size, and wherein the substrate is preferablya solid substrate.

The SLE markers of the arrangement/panel are fixed on the substrate,preferably spotted or immobilized, printed on or the like, in particularin a reproducible manner. One or more SLE markers can be presentmultiple times in the totality of all SLE markers and may be present indifferent quantities based on a spot. Furthermore, the SLE markers canbe standardised on the substrate (for example by means of serialdilution series of, for example, human globulins as internal calibratorsfor data normalisation and quantitative evaluation), A standard (forexample a gold standard) can also be applied to the substrate wherenecessary.

In a further embodiment, the SLE markers are present as clones. Suchclones can be obtained for example by means of a cDNA expression libraryaccording to the invention. In a preferred embodiment, such expressionlibraries are obtained using expression vectors from a cDNA expressionlibrary comprising the cDNAs of the SLE-specific marker sequences. Theseexpression vectors preferably contain inducible promoters. The inductionof the expression can be carried out for example by means of an inducer,such as IPTG. Suitable expression vectors are described in Terpe et al,(Terpe T Appl Microbiol Biotechnol. 2003 January; 60(5):523-33).

Expression libraries are known to a person skilled in the art; they canbe produced in accordance with standard works, such as Sambrook et ai,“Molecular Cloning, A laboratory handbook, 2^(nd) edition (1989), CSHpress, Cold Spring Harbor, Mew York. Expression libraries that aretissue-specific (for example human tissue, in particular human organs)are furthermore preferable. Further, expression libraries that can beobtained by means of exon trapping are also included in accordance withthe invention.

Protein arrays or corresponding expression libraries that do not exhibitany redundancy (what is known as a Uniclone® library) and that can beproduced for example in accordance with the teaching of WO 39/57311 andWO 99/57312 are furthermore preferred—These preferred Uniclone®libraries have a high proportion of non-defective fully expressedproteins of a cDNA expression library.

Within the scope of this invention, the clones can also be, but are notlimited to, transformed bacteria, recombinant phages or transformedcells of mammals, insects, fungi, yeasts or plants.

The clones are fixed, spotted or immobilised on a solid substrate. Theinvention therefore relates to an arrangement/use, wherein theSLE-specific markers are present as clones.

In addition, the SLE markers can be present in the respective form inthe form of a fusion protein, which for example contains at least oneaffinity epitope or “tag”, wherein the tag is selected for example fromc-myc, his tag, arg tag, FLAG, alkaline phosphatase, V5 tag, T7 tag orstrep tag, HAT tag, NusA, S tag, SBP tag, thioredoxin, DsbA, or thefusion protein has one or more additional domains for example, such as acellulose-binding domain, green fluorescent, protein, maltose-bindingprotein, calmodulin-binding protein, glutathione 3-transferase or lacZ.

In a further embodiment the invention relates to an assay, for example amultiplex assay, a bead-based assay, or protein array for identifyingand characterising a substance, for example a hit, a lead substance, oran active substance for SLE, Here, a substance to be tested is used,This can be any native or non-native biomolecule, a (synthetic) chemicalmolecule, a natural substance, a mixture or a substance library. Oncethe substance to be tested has contacted an SLE marker, the bindingsuccess is evaluated, for example with use of commercially availableimage-analysis software (GenePix Pro (Axon Laboratories), Aida(Raytest), ScanArray (Packard Bioscience).

Binding according to the invention, binding success, interactions, forexample protein-protein interactions (for example protein to SLE marker,such as antigen/antibody) or corresponding “means for detecting thebinding success” can be visualised for example by means of fluorescencelabelling, biotinylation, radio-isotope labelling or colloid gold orlatex particle labelling in the conventional manner. Bound antibodiesare detected with the aid of secondary antibodies, “which are labelledusing commercially available reporter molecules (for example Cy, Alexa,Dyomics, FITC or similar fluorescent dyes, colloidal gold or latexparticles), or with reporter enzymes, such as alkaline phosphatase,horseradish peroxidase, etc. and the corresponding colorimetric,fluorescent or chemoluminescent substrates. A readout is performed forexample by means of a microarray laser scanner, a. CCD camera orvisually.

In. a further embodiment, the invention relates to a drug or an activesubstance or prodrug for SLE, developed and obtainable by the use of anSLE marker according to the invention.

The invention also relates to the use of an SLE marker selected from,sequences SEQ ID No. 1 to 1587 and subsequences of SEQ ID No. 1 to 1587with at least 90%, preferably at least 95% of the length of SEQ ID No. 1to 1587 and homologues of SEQ ID No. 1 to 1587 and subsequences thereofwith an identity of at least 95%, preferably at least 98% or more, tothe corresponding sequences and proteins/peptides coded by the sequencesSEQ ID No. 1 to 1058, coded by the subsequences thereof and homologuesas affinity material for carrying out an apheresis or blood washing forpatients with SLE, i.e. apheresis of SLE autoantibodies, The inventionthus relates to the use of the markers according to the invention,preferably in the form of an arrangement, as affinity material forcarrying out an apheresis or a blood washing in the broader sense,wherein substances from bodily fluids from a patient with SLE, such asblood or plasma, bind to the markers according to the invention andconsequently can be removed selectively from the bodily fluid. Theapplication in blood washing is a special case of use of the SLE markersas a target. Devices for carrying out a blood washing, in particularimmunapheresis, are known to a person skilled in the art and can becarried out for example by means of dialysis.

The following examples and drawings explain the invention, but do notlimit the invention to the examples.

FIG. 1 shows a volcano plot of the relative antigen reactivities of theSLE patients compared to healthy controls.

FIG. 2 shows a volcano plot of the relative antigen reactivities of theSLE patients compared to RA patients.

FIG. 3: volcano plot of the antigen reactivities of SLE patientscompared with a combined group of patients with various autoimmunediseases, such as SSc (PSS), SPA, early rheumatoid arthritis and SPA,

FIG. 4 frequency of the autoantibody reactivities of selected antigensin SLE patients and healthy test subjects, A threshold value of 3 SOdeviations above the mean value of the healthy test, subject wasapplied. The threshold value for the antigen SNRNP was set to 2SD.

FIG. 5: volcano plot of the autoantibody reactivities of ENA-4-negativeSLE patients compared with healthy controls.

FIG. 6: receiver operating characteristic curves (ROCs) for thediagnosis of SLS compared to healthy test subjects and AID samples

FIG. 7: volcano plot for SLE lupus nephritis compared with SLE withoutlupus nephritis

FIG. 8: frequency of the lupus nephritis antigens in a model with nestedcross validation.

FIG. 9: dendogram of the SLE antigens following calculation ofSpearman/s rank correlation coefficient a) dendogram of the known ENA-4antigens and b) dendogram of 50 selected SLE antigens.

FIG. 10A: PPLS-DA biplot of the SLE patients and healthy controls withuse of the ENA-4 and ribosomal antigens.

FIG. 10B: PPLS-DA biplot of the SLE patients and healthy controls basedon 50 SLE antigens.

FIG. 11: calculated p-values of the antigens from Table 2 and also thefrequency of patients from a) SLE cohort I, b) SLE cohort II, and c) SLEcohort III who were classified as autoantibody-positive for thisantigen.

EXAMPLES Example 1: Selection of the SLE Patients and Test Subjects

Selection of the patient groups to be tested: Blood samples wereanalysed from 129 SLE patients, 100 patients with systemic sclerosis(SSc, PSS), 75 patients with rheumatoid arthritis (RA), 537 patientswith early RA (period of disease less than 6 months) and 75 patientswith ankylosing spondylitis (SPA)/Bekhterev's disease (SPA). 343 bloodsamples from the Bavarian Red Cross (RFC) were used as control group. Aninformed consent of the Ethics Commission of the clinical partners andof the biobank of the BRC was received from all test subjects.

TABLE 1 Patient samples and clinical data (test cohort. I) 2. Screen 1.Screen SSc (PSS) Early RA SLE RA Healthy SLE Total Subtype (<6 months)SPA Healthy Number 129 75 123 100 100  537   82   343   Age 39 +/− 56.6+/− 41.3 +/− 39.8 +/− 56.9 +/− Limited 56.8 +/− 43.7 +/− 47.7 +/−(years) 12 13.2 11 11.9 13.4 n − 50 14.3 10.1 11.7 % female 86.1 72 86.283 87 Diffuse 62.2 15.9 58.3 n = 32 % ANA 77.5 N.D. N.D. 100 95 OverlapN.D. N.D. N.D. n = 9 SLAM 7.7 +/− 7.7 +/− 5.1 5.1 SLICC 1.45 +/− 1.45+/− 1.8 1.8 ANA % ENA-4 37 48 positive % U1-RNP(% 13 13 of ENA-4 pos.)SM (% of 8 8 ENA-4 pos.) SS-A/Ro52 35 35 (% of ENA- 4 pos.) SS0B/Ro60 1010 (% of ENA- 4 pos.) Kidney 26.4 34 involvement %

Example 2: Antigen Production

Five cDNA libraries that had been produced from different human, tissues(foetal brain, intestine, lung, liver and T-cells) were used for theproduction, of the recombinant antigens. All cDNAs were expressed in E.coli under the transcriptional control of the lactose-induciblepromoter. The resultant proteins carry, at their amino terminus, anadditional sequence for a hexahistidine purification tag (His6 tag),Target, antigens which were not present, in the cDNA library wereproduced by chemical synthesis (Life Technologies) and cloned into theexpression vector pQE30-NST, which already codes an amino-terminal His6tag.

Following recombinant expression of the proteins, these were isolated indenaturising conditions and purified by means of metal affinitychromatography (IMAC). The proteins were lyophilised and stored set −20°C. until further use (http://www.lifesciences.sourceboioscience.com).

Example 3: Production of the BBAs

The production of BBAs was adapted to a microtitre plate format, suchthat 384 coupling reactions could be assessed in parallel usingautomated pipette systems (Starlet, Hamilton Robotics, Evo Freedom 130,Tecan), For the use of automated pipette systems, the individual beadregions were transferred into coupling pates (96 well Greiner) and theantigens were transferred into 2D barcode vessels (Thermo Scientific).For each coupling reaction, 0.6 to 2.5 million beads and, depending onthe antigen, 1 to 100 μg protein were used.

All washing and pipetting steps of the coupling reaction were carriedout in coupling plates which were fixed on magnets. The beads werewashed twice with 100 μl LxAP buffer (100 roM NaH2PO4, pH 6.2) and then,received in 120 μl LxAP buffer. For the activation, 15 μl1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC; 50 mg/ml) and 15 μlN-hydroxysulfosuccinimide (sulfo-NHS; 50 mg/ml) were added by pipette toform a bead suspension, and these suspensions were then incubated for 20minutes in the shaker (RT, 900 rpm, protected against light). Thebeads—were then washed 3× with 150 μl LxKPT buffer and then the proteinsolution was added. Following an incubation period of two hours in theshaker (RT, 300 rpm, protected against light), the beads were thenwashed three times with 150 μl LxKPT buffer. To block free bindingpoints, 100 ul LxCBSP buffer (PBS, 1% BSA, 0.05% ProClin300) were added,and these, mixtures were then incubated for 20 min in the shaker (RT,900 rpm, protected against, light). This was followed by incubation overnight at 4-8° C. The BBA was produced by the combination of beadscoupled to antigens and was stored at 4-8° C., protected against light,until use.

Example 4: Quality Control of the BBAs

In order to check the immobilisation of the proteins at the respectivebead regions, a coupling control, was carried out. Here, differentamounts of beads were used (250, 500 and 750 beads per bead region). Fora reaction mixture, 500 beads for example per bead region were dilutedin LxCBS buffer (PBS, 1% BSA) and transferred into an assay plate (96well half area microplate, Greiner).

Before each washing step, the assay plate with the beads was placed for2 minutes on a magnet, and the supernatant was then removed. After threewashing steps, the beads were incorporated with 100 μl LxWPT buffer(PBS, 0,05% Tween-20), and 10 μl/ml penta-his antibodies (Qiagen) orLxCBS buffer (PBS, 1% BSA) were added by pipette. Following incubationfor 45 minutes in the shaker (RT, 900 rpm, protected against light), thesupernatant was removed and the beads were washed in two steps, 5 μl/mlgoat, anti-mouse IgG-PE (Phycoerythrin) or goat anti-human IgG-PE(Dianova) were then added as secondary antibody to the reaction mixtureand incubated for 30 minutes. Following two washing steps, 100 μl ofcarrier liquid (Luminex) was added to the beads. The fluorescence signalof the beads was detected with the aid of the FlexMAPSD instrument.Here, the bead count on the one hand and the median of the fluorescenceintensity (MFI value) on the other hand were measured.

Example 5: Application of BBAs

For application, BBAs were incubated with sera and all IgG-basedautoantibodies bonded to antigens were detected with the aid of asecondary antibody. In order to enable a high throughput ofmeasurements, the application of BBAs was adapted to a microtiter plateformat so that either an 8-channel (Starlet, Hamilton Robotics) or a96-channel (Evo Freedom. 150, Tecan) automated pipetting system could beused. The sera to be examined were transferred into 2D barcode vesselsand then diluted 1:100 with assay buffer (PBS, 0,5% BSA, 10% E. colilysate, 50% low-cross buffer (Candor Technologies)). In order toneutralise human antibodies directed against E. coli, a pre-incubationof the sera dilutions was performed for 20 min. In this time, 500 beadsper bead region were distributed in the assay plate. 50 μl of dilutedserum were added to the beads in the coupling plate, and the reactionmixtures were incubated for 18-22 h in the shaker (4-8 *C, 900 rpm,protected against light). After three washing steps in each case with100 μl LxWPT buffer, 5 μl/ml of the detection antibody goat anti-humanIgG-PE (Dianova) were added to the reaction mixtures and incubated for 1h in the shaker (RT, 900 rpm). The beads were then washed three timeswith 100 pi LxWPT and incorporated in 100 μl carrier liquid (Luminex).The fluorescence signal of the beads was detected with the aid of theFiexMAF3D instrument, Here, the bead count on the one hand and the MFIvalue (median fluorescence intensity) on the other hand were measured.

Example 6: Biostatistical Analysis

The biostatistical analysis comprised univariate and multivariatemethods for describing the statistical properties of individual antigensand of groups of antigens. In order to discover interesting candidatesfor panels, the key property was a good separation between the groups ofsamples based on the MFI values. In order to find antigen candidates forpanel generation, univariate testing, receiver operating characteristic(ROC) analyses, correlation profiles, powered partial least squaresdiscriminant analysis (PPLS-DA) and random forests were used as methods.Biostatistical analyses were subject to expert assessment, in order todefine final antigen panels.

Before the statistical analysis, the MFI values were log 2-transformedin order to reduce the skew in the distributions. If more than 20% ofthe values ‘were missing, antigens were excluded from the analysis.Missing values—were replaced by median imputation. A quant lienormalisation was carried out under consideration of the reference serain order to normalise, per BBA set, all measured samples on individualplates.

Besides descriptive standardisation for MFI values, non-parametric testswere also carried out with the aid of the two-sided Mann-Whitney-U testin order to uncover differences in the median values of the groups. Thetest level for multiple testing was corrected in accordance with theBonferroni-Holm procedure. In addition, the Benjamin-Hochberg procedureinclusive of the determination of the False Discovery Rate (FDR,q-value) was applied. In addition, fold-change and effect size weredetermined. In order to assess the classification quality, an ROCanalysis was carried out, within the scope of which sensitivity,specificity and the area under the ROC curve (AUC) were calculated, ineach case inclusive of the 95% confidence interval on the basis of thebootstrap method. Boxplots and volcano plots were used, for graphicalrepresentation. A scoring system was implemented on the basis of theunivariate results.

By means of the application of a PPLS-DA, it was attempted to maximisethe correlation between the component of the response matrix. A lineardiscriminant analysis with the latent component as predictors was usedfor the final classification, A random forest was applied, in whichbinary decision trees are combined. The decision trees were formed onthe basis of a number of bootstrap samples of a training sample and byrandom selection of a subgroup of explaining variables at each node. Thenumber of input variables, which was selected randomly with eachdivision step, was determined as the square root of the total number ofvariables, and the number of trees in the random forest was set to 1000.A cross validation with 500 times throughput was imp I. erne n t ed forboth multi-variant approaches.

Example 7: Autoantibodies/Antigen Reactivities Differentiate SLE fromHealthy Controls, Rheumatoid Arthritis and Other Autoimmune Diseases

In a first screening the antigen reactivities of 129 SLE patients, 75 RApatients, and 134 healthy controls categorized in accordance with ageand sex were differentially tested. For this purpose, the autoantibodyreactivities of these blood samples were tested on 5857 antigens coupledto Luminex beads. In order to identify antigens with which the group ofall SLE patients can be distinguished from different control croupsconsisting of healthy samples and patients with RA, univariatestatistical tests were carried out, The result, of the statistical testis illustrated as a volcano plot for all 5857 antigens. In the volcanoplot, the x-axis shows the relative change of the antigen reactivity inSLE patients compared with healthy controls (FIG. 1) and RA patients(FIG. 2). The y-axis presents the p-value of the statistical tests.FIGS. 1 and 2 show that specific autoantibody reactivities were foundwhich are increased in the group of ail SLE and which can distinguishboth from healthy donors and from RA patients.

Example 8: Autoantibodies/Antigen Reactivities Differentiate SLE fromHealthy Controls, Early Rheumatoid Arthritis and Other AutoimmuneDiseases

In a second screening with 6088 antigens, the antigens whichdifferentiate between healthy controls and donors with rheumatoidarthritis were tested on patients with early rheumatoid arthritis, SScand SPA., This is of importance in particular since patients withcollagenoses and mixed collagenoses have an overlapping autoantibodyprofile and therefore are difficult to diagnose, particularly in theearly phase

FIG. 3 shows a volcano plot of the antigen reactivities of SLE patientsagainst a combined group of patients with various autoimmune diseases,such as SSc, SPA, early rheumatoid arthritis, and SPA.

Following univariate statistical evaluation, a threshold value of p<0.05and a 1,5 times modified reactivity compared with the control group wereapplied. A final list of antigen reactivities over both screens wasestablished (Table 2).

In order to analyse the frequency of the newly identified antigens incomparison with, known antigens, a threshold value of 3 standarddeviations (SD) above the mean value of the healthy samples was defined.

Astonishingly, at least 4 additional antigens were identified of whichthe frequency in SLE patients lies above 15%. These include TMPO (19%)(SEQ ID No. 13), HNRNPA1 (26%) (SEQ ID No. 5), XRCC5 (15%) (SEQ ID No.22) and MVP (15%) (SEQ ID No. 7).

FIG. 4 shows the frequency of 23 antigens in comparison to the healthycontrols.

Table 2 summarises the identified antigen reactivities and differentgroup comparisons.

TABLE 2 List of all antigen reactivities Statistical Test SEQ Gene GeneGene Panel SLE ENA-4 neg L. Nephr. SLE ID No. ID Symbol Name Group SLEL. Nephr. Cluster vs HV vs SLE vs control 1 1629 DBT dihydrolipoamide 1x x SLE branched chain vs transacylase E2 AID 2 1737 DLATdihydrolipoamide S- 1 x SLE acetyltransferase vs AID 3 7430 EZR ezrin 1x x x SLE vs AID 4 3017 HIST1H2BD histone cluster 1, 1 x x SLE H2bd vsAID 5 3178 HNRNPA1 heterogeneous 1 x x SLE nuclear vs ribonucleoproteinA1 AID 6 3181 HNRNPA2B1 heterogeneous 1 x x SLE nuclear vsribonucleoprotein AID A2/B1 7 9961 MVP major vault protein 1 x x x x SLEvs AID 8 6175 RPLP0 ribosomal protein, 1 x x x SLE large, P0 vs AID 96176 RPLP1 ribosomal protein, 1 x x x x SLE large, P1 vs AID 10 6181RPLP2 ribosomal protein, 1 x x x SLE large, P2 vs AID 11 30011 SH3KBP1SH3-domain kinase 1 x x SLE binding protein 1 vs AID 12 6625 SNRNP70small nuclear 1 x SLE ribonucleoprotein vs 70 kDa (U1) AID 13 6628 SNRPBsmall nuclear 1 x x x SLE ribonucleoprotein vs polypeptides B and AID B114 6638 SNRPN small nuclear 1 x SLE ribonucleoprotein vs polypeptide NAID 15 6672 SP100 SP100 nuclear 1 x x SLE antigen vs AID 16 6710 SPTBspectrin, beta, 1 x x SLE erythrocytic vs AID 17 6741 SSB Sjogrensyndrome 1 x x SLE antigen B vs (autoantigen La) AID 18 7112 TMPOthymopoietin 1 x x x SLE vs AID 19 6737 TRIM21 tripartite motif- 1 x x xSLE containing 21 vs AID 20 6738 TROVE2 TROVE domain family, 1 x x SLEmember 2 vs RA 21 7431 VIM vimentin 1 x x SLE vs AID 22 7520 XRCC5 X-rayrepair 1 x x SLE complementing vs defective repair in AID Chinesehamster cells 5 (double- strand-break re joining) 23 7764 ZNF217 zincfinger protein 1 x x SLE 217 vs AID 24 64763 ZNF574 zinc finger protein1 x x SLE 574 vs AID 25 148741 ANKRD35 ankyrin repeat 2 x x SLE domain35 vs HV 26 84779 ARD1B ARD1 homolog B 2 x x SLE (S. cerevisiae) vs AID27 672 BRCA1 breast cancer 1, 2 x x SLE early onset vs HV 28 134359C5orf37 chromosome 5 open 2 x x x SLE reading frame 37 vs HV 29 9478CABP1 calcium binding 2 x x SLE protein 1 vs HV 30 90557 CCDC74Acoiled-coil domain 2 x x SLE containing 74A vs HV 31 9973 CCS copperchaperone for 2 x x x x SLE superoxide dismutase vs AID 32 1410 CRYABcrystallin, alpha B 2 x x SLE vs HV 33 55802 DCP1A DCP1 decapping 2 x xSLE enzyme homolog A vs (S. cerevisiae) HV 34 79147 FKRP fukutin related2 x SLE protein vs HV 35 26128 KIAA1279 KIAA1279 2 x x SLE vs HV 3657608 KIAA1462 KIAA1462 2 x x SLE vs HV 37 1939 LGTN ligatin 2 x x SLEvs HV 38 84298 LLPH LLP homolog, long- 2 x x SLE term synaptic vsfacilitation HV (Aplysia) 39 11253 MAN1B1 mannosidase, alpha, 2 x x SLEclass 1B, member 1 vs HV 40 84930 MASTL microtubule 2 x x SLE associatedvs serine/threonine HV kinase-like 41 54531 MIER2 mesorm induction 2 x xx x SLE early response 1, vs family member 2 RA 42 4594 MUTmethylmalonyl 2 x x SLE Coenzyme A mutase vs HV 43 399687 myO18A myosinXVIIIA 2 x x SLE vs HV 44 8883 NAE1 NEDD8 activating 2 x x SLE enzyme E1and vs subunit 1 HV 45 10458 BAIAP2 BAI1-associated 2 x x SLE protein 2vs HV 46 4869 NPM1 nucleophosim 2 x x SLE (nucleolar vs phosphoproteinB23, HV numatrin) 47 5223 PGAM1 phosphoglycerate 2 x x SLE mutase 1(brain) vs HV 48 11040 PIM2 pim-2 oncogene 2 x x SLE vs HV 49 54517 PUS7pseudouridylate 2 x x SLE synthase 7 homolog vs (S. cerevisiae) HV 506605 SMARCE1 SWI/snf related, 2 x x SLE matrix associated, vs actindependent AID regulator of chromatin, subfamily e, member 1 51 23635SSBP2 single-stranded DNA 2 x x x SLE binding protein 2 vs HV 52 83660TLN2 talin 2 2 x x SLE vs HV 53 51673 TPPP3 tubulin 2 x x SLEpolymerization- vs promoting protein HV family member 3 54 7265 TTC1tetratricopeptide 2 x x SLE repeat domain 1 vs HV 55 124930 ANKRD13Bankyrin repeat 3 x SLE domain 13B vs HV 56 160 AP2A1 adaptor-related 3 xSLE protein complex 2, vs alpha 1 subunit HV 57 53335 BCL11A B-cellCLL/lymphoma 3 x x 11A (zinc finger protein) 58 79959 CEP76 centrosomalprotein 3 x 76 kDA 59 1153 CIRBP cold inducible RNA 3 x SLE bindingprotein vs HV 60 51084 CRYL1 crystallin, lambda 1 3 x 61 55827 DCAF6DDB1 and CUL4 3 x x x SLE associated factor 6 vs AID 62 6993 DYNLT1dynein, light chain, 3 x SLE Tctex-type 1 vs HV 63 283991 FAM100B familywith sequence 3 x SLE similarity 100, vs member B HV 64 9815 GIT2 Gprotein-coupled 3 x SLE receptor kinase vs interacting ArfGAP 2 HV 6584706 GPT2 glutamic pyruvate 3 x transaminase (alanine aminotransferase)2 66 3059 HCLS1 hematopoieti cell- 3 x x SLE specific Lyn vs substrate 1AID 67 3329 HSPD1 heat shock 60 kDa 3 x protein 1 (chaperonin) 68 3490IGFBP7 insulin-like growth 3 x SLE factor binding vs protein 7 HV 6923392 KIAA0368 KIAA0368 3 x 70 84695 LOXL3 lysyl oxidase-like 3 x 3 714133 MAP2 microtubule- 3 x SLE associated protein vs 2 HV 72 6837 MED22mediator complex 3 x subunit 22 73 29079 MED4 mediator complex 3 x xsubunit 4 74 10933 MORF4L1 mortality factor 4 3 x like 1 75 64963 MRPS11mitochondrial 3 x x SLE ribosomal protein vs HV 76 81565 NDEL1 nudEnuclear 3 x distribution gene E homolog (A. nidulans)-like 1 77 57447NDRG2 NDRG family member 3 x SLE 2 vs HV 78 4744 NEFH neurofilament,heavy 3 x polypeptide 79 153478 PLEKHG4B pleckstrin homology 3 x domaincontaining, family G (with RhoGef domain) member 4B [homo sapiena(human)] 80 11054 OGFR opioid growth factor 3 x x SLE receptor vs AID 8156122 PCDHB14 protocadherin beta 3 x SLE 14 vs HV 82 2923 PDIA3 proteindisulfide 3 x SLE isomerase family A, vs member 3 HV 83 23646 PLD3phospholipase D 3 x SLE family, member 3 vs HV 84 23759 PPIL2peptdylprolyl 3 x x isomerase (cyclophilin)-like 2 85 5557 PRIM1primase, DNA, 3 x SLE polypeptide 1 vs (49 kDa) HV 86 5682 PSMA1proteasome (prosome, 3 x SLE macropain) subunit, vs alpha type, 1 HV 875802 PTPRS protein tyrosine 3 x SLE phosphatase, vs receptor type, S HV88 81890 QTRT1 queuine tRNA- 3 x SLE ribosyltransferase 1 vs HV 89116362 RBP7 retinol binding 3 x SLE protein 7, cellular vs HV 90 10287RGS19 regulator of G- 3 x x protein signaling 19 91 83642 RP3-402G11.5selenoprotein O 3 x SLE vs HV 92 6389 SDHA succinate 3 x x SLEdehydrogenase vs complex, subunit A, AID flavoprotein (Fp) 93 54437SEMA5B sema domain, seven 3 x thrombospondin repeats (type 1 and type1-like), transmembrane domain (TM) and short cytoplasmic domain,(semaphorin) 5B 94 59343 SENP2 SUMO1/sentrin/SMT3 3 x SLE specificpeptidase vs 2 HV 95 6629 SNRPB2 small nuclear 3 x SLE ribonucleoproteinvs polypeptide B″ AID 96 27131 SNX5 sorting nexin 5 3 x SLE vs HV 979021 SOCS3 suppressor of 3 x x SLE cytokine signaling vs 3 HV 98 3925STMN1 stathmin 1 3 x SLE vs HV 99 81551 STMN4 stathmin-like 4 3 x SLE vsHV 100 27097 TAFSL TAF5-like RNA 3 x SLE polymerase II, vsp300/CBP-associated HV factor (PCAF)- associated factor, 65 kDa 10179521 TCEAL4 transcription 3 x SLE elongation factor A vs (SII)-like 4HV 102 10040 TOM1L1 target of mybl 3 x SLE (chicken)-like 1 vs HV 10322974 TPX2 TPX2, microtubule- 3 x SLE associated, homolog vs (Xenopuslaevis) HV 104 51567 TTRAP TRAF and TNF 3 x receptor associated protein105 8615 USO1 US01 homolog, 3 x x vescicle docking protein (yeast) 10610869 USP19 ubiquitin specific 3 x SLE peptidase 19 vs RA 107 29761USP25 ubiquitin specific 3 x peptidase 25 108 375690 WASH5P WAS proteinfamily 3 x x SLE homolog 5 vs pseudogene HV 109 10413 YAP1Yes-associated 3 x protein 1, 65 kDa 110 653121 ZBTB8A zinc finger andBTB 3 x x SLE domain containing vs BA HV 111 55311 ZNF444 zinc fingerprotein 3 x 444 112 29 ABR active BCR-related 4 x SLE gene vs AID 113118 ADD1 adducin 1 (alpha) 4 x SLE vs AID 114 55256 ADI1 acireductone 4x SLE dioxygenase 1 vs HV 115 9255 AIMP1 aminoacyl tRNA 4 x synthetasecomplex- interacting multifunctional protein 1 116 54522 ANKRD16 ankyrinrepeat 4 x SLE domain 16 vs HV 117 348 APOE apolipoprotein E 4 x SLE vsHV 118 64333 ARHGAP9 Rho GTPase 4 x SLE activating protein vs 9 HV 11922994 AZI1 5-azacytidine 4 SLE induced 1 vs HV 120 55971 BAIAP2L1BAI1-associated 4 x protein 2-like 1 121 7919 BAT1 HLA-B associated 4 xSLE transcript 1 vs RA 122 6046 BRD2 bromodomain 4 x containing 2 12356912 C11orf60 chromosome 11 open 4 x reading frame 60 124 79415C17orf62 chromosome 17 open 4 x reading frame 62 125 51300 C3orf1chromosome 3 open 4 x SLE reading frame 1 vs RA 126 128866 CHMP4Bchromatin modifying 4 x SLE protein 4B vs AID 127 23122 CIC capicuahomolog 4 x SLE (Drosophila) vs AID 128 10970 CKAP4 cytoskeleton- 4 xSLE associated protein vs 4 HV 129 23122 CLASP2 cytoplasmic linker 4 xassociated protein 2 130 1311 COMP cartilage 4 x oligomeric matrixprotein 131 7812 CSDE1 cold shock domain 4 x SLE containing E1, RNA- vsbinding HV 132 8642 DCHS1 dachsous 1 4 x SLE (Drosophila) vs AID 1339909 DENND4B DENN/MADD domain 4 x x containing 4B 134 1743 DLSTdihydrolipoamide S- 4 x succinyltransferase (E2 component of 2-oxo-glutarate complex) 135 84444 DOT1L DOT1-like, histone 4 x H3methyltransferase (S. cerevisiae) 136 51143 DYNC1LI1 dynein, cytoplasmic4 x SLE 1, light vs intermediate chain 1 HV 137 51011 FAHD2Afumarylacetoacetate 4 x hydrolase domain containing 2A 138 92689FAM114A1 family with sequence 4 x similarity 114, member A1 139 54463FAM134B family with sequence 4 x similarity 134, member B 140 100129583FAM47E family with sequence 4 x SLE similarity 47, vs member E HV 14193611 FBXO44 F-box protein 44 4 x 142 60681 FKBP10 FK506 binding 4 x SLEprotein 10, 65 kDa vs AID 143 23360 FNBP4 formin binding 4 x protein 4144 2300 FOXL1 forkhead box L1 4 x SLE vs HV 145 64689 GORASP1 golgireassembly 4 x SLE stacking protein 1, vs 65 kDa AID 146 2934 GSNgelsolin 4 x SLE (amyloidosis, vs Finnish type) HV 147 3039 HBA1hemoglobin, alpha 4 x 148 3040 HBA2 hemoglobin, alpha 2 4 x 149 38858HES5 hairy and enhancer 4 x of split 5 (Drosophilia) 150 10525 HYOU1hypoxia up-regulated 4 x 1 151 3608 ILF2 interleukin enhancer 4 x SLEbinding factor 2, vs 45 kDa RA 152 23135 KDM6B lysine (K)-specific 4 xSLE demethylasae 6B vs AID 153 56243 KIAA1217 KIAA1217 4 x SLE vs HV 15457662 KIAA1543 KIAA1543 4 x 155 57498 KIDINS220 kinase D-interacting 4 xsubstrate, 220 kDA 156 3855 KRT7 keratin 7 4 x SLE vs HV 157 729970LOC729970 similar to 4 x hCG2028352 158 9935 MAFB v-maf 4 xmusculoaponeurotic fibrosarcoma oncogene homolog B (avian) 159 23764MAFF v-maf 4 x SLE musculoaponeurotic vs fibrosarcoma HV oncogenehomolog F (avian) 160 22924 MAPRE3 microtubule- 4 x associated protein,RP/EB family, member 3 161 8079 MLF2 myeloid leukemia 4 x factor 2 1624676 NAP1L4 nucleosome assembly 4 x protein 1-like 4 163 4688 NCF2neutrophil cytosolic 4 x SLE factor 2 vs HV 164 4780 NFE2L2 nuclearfactor 4 x (erythroid-derived 2)-like 2 165 79840 NHEJ1 nonhomologousend- 4 x x joining factor 1 166 22861 NLRP1 NLR family, pyrin 4 x SLEdomain containing 1 vs HV 167 65009 NDRG4 NDRG family member 4 4 x SLEvs HV 168 4841 NONO non-POU domain 4 x SLE containing, octamer- vsbinding AID 169 29982 NRBF2 nuclear receptor 4 x SLE binding factor 2 vsAID 170 8439 NSMAF neutral 4 x SLE sphingomyelinase (N- vsSMase)activation HV associated factor 171 4926 NUMA1 nuclear mitotic 4 xSLE apparatus protein 1 vs RA 172 84759 PCGF1 polycomb group ring 4 xfinger 1 173 84306 PDCD2L programmed cell 4 x SLE death 2-like vs HV 1745195 PEX14 peroxisomal 4 x SLE biogenesis factor 14 vs HV 175 9091 PIGQphosphatidylinositol 4 x SLE glycan anchor vs biosynthesis, class RA Q176 100137049 PLA2G4B phospholipase A2, 4 x SLE group IVB vs (cytosolic)RA 177 10226 PLIN3 perilipin 3 4 x 178 5373 PMM2 phosphomannomutase 2 4x 179 10450 PPIE peptidylprolyl 4 x isomerase E (cyclophilin E) 180 5694PSMB6 proteasome (prosome, 4 x macropain) subunit, beta type, 6 18122913 RALY RNA binding protein, 4 x SLE autoantigenic vs(hnRNP-associated HV with lethal yellow homolog (mouse)) 182 8241 RBM10RNA binding motif 4 x protein 10 183 9904 RBM19 RNA binding motif 4 xSLE protein 19 vs HV 184 9743 RICS Rho GTPase- 4 x activating protein185 8780 RIOK3 RIO kinase 3 (yeast) 4 x 186 8578 SCARF1 scavengerreceptor 4 x SLE class 4, member 1 vs AID 187 23513 SCRIB scribbledhomolog 4 x SLE (Drosophila) vs HV 188 644096 SDHAF1 succinate 4 x SLEdehydrogenase vs complex assembly RA factor 1 189 57794 SF4 splicingfactor 4 4 x SLE vs RA 190 9814 SFI1 Sfi1 homolog, 4 x spindle assemblyassociated (yeast) 191 6421 SFPQ splicing factor 4 x SLEproline/glutamine- vs rich (polypyrimidine AID tract binding proteinassociated) 192 83442 SH3BGRL3 SH3 domain binding 4 x glutamic acid-richprotein like 3 193 6461 SHB Src homology 2 4 x SLE domain containing vsadaptor protein B AID 194 23381 SMG5 Smg-5 homolog, 4 x SLE nonsensemediated vs mRNA decay factor HV (C. elegans) 195 112574 SNX18 sortingnexin 18 4 x SLE vs HV 196 84501 SPIRE2 spire homolog 2 4 x SLE(Drosophila) vs HV 197 54961 SSH3 slingshot homolog 3 4 x SLE(Drosophila) vs AID 198 9263 STK17A serine/threonine 4 x kinase 17a 19951111 SUV420H1 suppressor of 4 x variegation 4-20 homolog 1 (Drosophila)200 6902 TBCA tubulin folding 4 x cofactor A 201 7024 TFCP2transcription factor 4 x SLE CP2 vs HV 202 7030 TFE3 transcriptionfactor 4 x SLE binding to IGHM vs enhancer 3 HV 203 90326 THAP3 THAPdomain 4 x SLE containing, vs apoptosis associated AID protein 3 20410043 TOM1 target of myb1 4 x (chicken) 205 7168 TPM1 tropomyosin 1 4 xSLE (alpha) vs HV 206 54952 TRNAU1AP tRNA selenocysteine 4 x 1associated protein 1 207 26140 TTLL3 tubulin tyrosine 4 x ligase-likefamily, member 3 208 7371 UCK2 uridine-cytidine 4 x SLE kinase 2 vs HV209 9277 WDR46 WD repeat domain 46 4 x SLE vs HV 210 55100 WDR70 WDrepeat domain 70 4 x SLE vs AID 211 23038 WDTC1 WD and 4 x SLEtetratricopeptide vs repeats 1 HV 212 9831 ZNF623 zinc finger protein 4x 623 213 79364 ZXDC ZXD family zinc 4 x x SLE finger C vs AID 214 7791ZYX zyxin 4 x SLE vs AID 215 55964 SEPT3 septin 3 5 X 216 5413 SEPT5septin 5 5 x 217 26574 AATF apoptosis 5 x antagonizing transcriptionfactor 218 91703 ACY3 aspartoacylase 5 x (aminocyclase) 3 219 9509ADAMTS2 ADAM 6 SLE metallopeptidase vs with thrombospondin RA type 1motif, 2 220 10939 AFG3L2 AFG3 ATPase family 6 SLE gene 3-like 2 vs(yeast) HV 221 1646 AKR1C2 aldo-keto reductase 6 SLE family 1, member C2vs (dihydrodiol RA dehydrogenase 2; bile acid binding protein; 3-alphahydroxysteroid dehydrogenase, type III) 222 267 AMFR autocrine motility6 SLE factor receptor vs RA 223 10777 ARPP-21 cyclic AMP-regulated 6 SLEphosphoprotein, 21 vs kD RA 224 421 ARVCF armadillo repeat 6 SLE genedeletes in vs velocardiofacial RA syndrome 225 80150 ASRGL1 asparaginaselike 1 6 SLE vs RA 226 539 ATP50 ATP synthase, H+ 6 SLE transporting, vsmitochondrial F1 RA complex, O subunit 227 79870 BAALC brain and acute 6SLE leukemia, vs cytoplasmic RA 228 9531 BAG3 BCL2-associated 5 xathanogene 3 229 9275 BCL7B B-cell CLL/lymphoma 6 SLE 7B vs HV 230 55108BSDC1 BSD domain 6 SLE containing 1 vs AID 231 54934 C12orf41 chromosome12 open 6 SLE reading frame 41 vs RA 232 55049 C19orf60 chromosome 19open 6 SLE reading frame 60 vs RA 233 388799 C20orf107 chromosome 20open 5 x reading frame 107 234 149840 C20orf196 chromosome 20 open 6 SLEreading frame 196 vs RA 235 51507 C20orf43 chromosome 20 open 6 SLEreading frame 43 vs RA 236 55684 C9orf86 chromosome 9 open 6 SLE readingframe 86 vs HV 237 23523 CABIN1 calcineurin binding 6 SLE protein 1 vsRA 238 157922 CAMSAP1 calmodulin regulated 6 SLE spectrin-associated vsprotein 1 RA 239 23624 CBLC Cas-Br-M (murine) 6 SLE ecotropic retroviralvs transforming HV sequence c 240 124808 CCDC43 coiled-coil domain 6 SLEcontaining 43 vs RA 241 100133941 CD24 CD24 molecule 5 x 242 11140 CDC37cell division cycle 6 SLE 37 homolog vs (S. cerevisiae) RA 243 10153CEBPZ CCAAT/enhancer 6 SLE binding protein vs (C/EBP), zeta RA 244 51510CHMP5 chromatin modifying 6 SLE protein 5 vs RA 245 63922 CHTF18 CTF18,chromosome 5 x transmission fidelity factor 18 homolog (S. cerevisiae)246 51727 CMPK1 cytidine 6 SLE monophosphate (UMP- vs CMP) kinase 1, AIDcytosolic 247 64708 COPS7B COP9 constitutive 5 x photomorphogenichomolog subunit 7B (Arabidopsis) 248 51117 COQ4 coenzyme Q4 homolog 6SLE (S. cerevisiae) vs RA 249 27254 CSDC2 cold shock domain 5 xcontaining C2, RNA binding 250 162989 DEDD2 death effector 6 SLE domaincontaining 2 vs RA 251 9704 DHX34 DEAH (Asp-Glu-Ala- 6 SLE His) boxpolypeptide vs 34 RA 252 55837 EAPP E2F-associated 6 SLE phosphoproteinvs RA 253 1915 EEF1A1 eukaryotic 6 SLE translation vs elongation factor1 RA alpha 1 254 1936 EEF1D eukaryotic 6 SLE translation vs elongationfactor 1 RA delta (guanine nucleotide exchange protein) 255 8669 EIF3Jeukaryotic 6 SLE translation vs initiation factor 3, RA subunit J 25655740 ENAH enabled homolog 6 SLE (Drosophila) vs HV 257 2023 ENO1enolase 1, (alpha) 6 SLE vs HV 258 11124 FAF1 Fas (TNFRSF6) 5 xassociated factor 1 259 11170 FAM107A family with sequence 6 SLEsimilarity 107, vs member A HV 260 84908 FAM136A family with sequence 6SLE similarity 136, vs member A RA 261 10144 FAM13A family with sequence6 SLE similarity 13, vs member A RA 262 26017 FAM32A family withsequence 6 SLE similarity 32, vs member A HV 263 64762 FAM59A familywith sequence 6 SLE similarity 59, vs member A RA 264 150946 FAM59Bfamily with sequence 6 SLE similarity 59, vs member B HV 265 83706FERMT3 fermitin family 6 SLE homolog 3 vs (Drosophila) RA 266 23307FKBP15 FK506 binding 6 SLE protein 15, 133 kDa vs HV 267 2670 GFAP glialfibrillary 6 SLE acidic protein vs RA 268 51031 GLOD4 glyoxalase domain6 SLE containing 4 vs AID 269 81488 GRINL1A glutamate receptor, 6 SLEionotropic, N-methyl vs D-aspartate-like 1A RA 270 2922 GRPgastrin-releasing 6 SLE peptide vs RA 271 2935 GSPT1 G1 to S phase 6 SLEtransition 1 vs RA 272 93323 HAUS8 HAUS augmin-like 6 SLE complex,subunit 8 vs HV 273 3054 HCFC1 host cell factor C1 6 SLE (VP16-accessoryvs protein) AID 274 3069 HDLBP high density 6 SLE lipoprotein binding vsprotein RA 275 3184 HNRNPD heterogenous nuclear 6 SLE ribonucleoproteinD vs (AU-rich element RNA HV binding protein 1, 37 kDa) 276 3320HSP90AA1 heat shock protein 6 SLE 90 kDa alpha vs (cytosolic), class ARA member 1 277 7184 HSP90B1 heat shock protein 6 SLE 90 kDa beta(Grp94), vs member 1 RA 278 3304 HSPA1B heat shock 70 kDa 6 SLE protein1B vs RA 279 3315 HSPB1 heat shock 27 kDa 4 x x SLE protein 1 vs RA 2805654 HTRA1 HtrA serine 6 SLE peptidase 1 vs RA 281 3382 ICA1 islet cell6 SLE autoantigen 1, 69 kDa vs RA 282 3550 IK IK cytokine, down- 6 SLEregulator of HLA II vs HV 283 80895 ILKAP integrin-linked 6 SLEkinase-associated vs serine/threonine RA phosphatase 2C 284 84162KIAA1109 KIAA1109 6 SLE vs AID 285 3856 KRT8 keratin 8 6 SLE vs RA 28623367 LARP1 La ribonucleoprotein 6 SLE domain family, vs member 1 AID287 4001 LMNB1 lamin B1 6 SLE vs RA 288 79888 LPCAT1lysophosphatidylcholine 5 x SLE acyltransferase vs 1 HV 289 10916 MAGED2melanoma antigen 5 x family D, 2 290 55700 MAP7D1 MAP7 domain 6 SLEcontaining 1 vs RA 291 5602 MAPK10 mitogen-activated 6 SLE proteinkinase 10 vs HV 292 22919 MAPRE1 microtubule- 6 SLE associated protein,vs RP/EB family, member AID 1 293 4137 MAPT microtubule- 6 SLEassociated protein, vs tau RA 294 23139 MAST2 microtubule 6 SLEassociated vs serine/threonine RA kinase 2 295 53615 MBD3 methyl-CpGbinding 6 SLE domain protein 3 vs RA 296 56922 MCCC1 methylcrotonoyl- 6SLE Coenzyme A vs carboxylase 1 HV (alpha) 297 1953 MEGF6 multipleEGF-like- 6 SLE domains 6 vs RA 298 4302 MLLT6 myeloid/lymphoid or 6 SLEmixed-lineage vs leukemia (trithorax RA homolog, Drosophila);translocated to, 6 299 10200 MPHOSPH6 M-phase 6 SLE phosphoprotein 6 vsRA 300 10240 MRPS31 mitochondrial 6 SLE ribosomal protein vs S31 HV 30184939 MUM1 melanoma associated 5 x antigen (mutated) 1 302 4599 MX1myxovirus (influenza 6 SLE virus) resistance 1, vs interferon-inducibleRA protein p78 (mouse) 303 4716 NDUFB10 NADH dehydrogenase 6 SLE(ubiquinone) 1 beta vs subcomplex, 10, RA 22 kDa 304 4796 NFKBIL2nuclear factor of 6 SLE kappa light vs polypeptide gene HV enhancer inB-cells inhibitor-like 2 305 11188 NISCH nischarin 6 SLE vs RA 306 10381TUBB3 tubulin, beta 3 6 SLE class III vs RA 307 8602 NOP14 NOP14nucleolar 6 SLE protein homolog vs (yeast) RA 308 9722 NOS1AP nitricoxice 6 synthase 1 (neuronal) adaptor protein 309 29959 NRBP1 nuclearreceptor 5 x binding protein 1 310 142 PARP1 poly (ADP-ribose) 6 SLEpolymerase 1 vs RA 311 5091 PC pyruvate 6 SLE carboxylase vs RA 31223024 PDZRN3 PDZ domain 6 SLE containing ring vs finger 3 RA 313 8682PEA15 phosphoprotein 6 SLE enriched in vs astrocytes 15 RA 314 5187 PER1period homolog 1 6 SLE (Drosophila) vs HV 315 57649 PHF12 PHD fingerprotein 5 x 12 316 26227 PHGDH phosphoglycerate 5 x dehydrogenase 3171263 PLK3 polo-like kinase 3 6 SLE (Drosophila) vs RA 318 23654 PLXNB2plexin B2 6 SLE vs RA 319 56902 PNO1 partner of NOB1 6 SLE homolog vs(S. cerevisiae) RA 320 5479 PPIB peptidylprolyl 6 SLE isomerase B vs(cyclophilin B) HV 321 56978 PRDM8 PR domain 6 SLE containing 8 vs HV322 55119 PRPF38B PRP38 pre-mRNA 6 SLE processing factor vs 38 (yeast)domain RA containing B 323 5764 PTN pleiotrophin 6 SLE vs HV 324 5819PVRL2 poliovirus 5 x receptor-related 2 (herpesvirus entry mediator B)325 5831 PYCR1 pyrroline-5- 6 SLE carboxylate vs reductase 1 RA 32665997 RASL11B RAS-like, family 6 SLE 11, member B vs RA 327 55658 RNF126ring finger protein 6 SLE 126 vs AID 328 115992 RNF166 ring fingerprotein 6 SLE 166 vs HV 329 9025 RNF8 ring finger protein 6 SLE 8 vs HV330 6092 ROBO2 roundabout, axon 5 x guidance receptor, homolog 2(Drosophila) 331 64221 ROBO3 roundabout, axon x guidance receptor,homolog 3 (Drosophila) 332 4736 RPL10A ribosomal protein 6 SLE L10a vsRA 333 6152 RPL24 robosomal protein 6 SLE L24 vs RA 334 148418 SAMD13sterile alpha motif 6 SLE domain containing vs 13 HV 335 57147 SCYL3SCY1-like 3 6 SLE (S. cerevisiae) vs AID 336 6382 SDC1 syndecan 1 6 SLEvs RA 337 91461 SGK493 protein kinase-like 5 x protein SgK493 338 6449SGTA small glutamine- 6 SLE rich vs tetratricopeptide HV repeat (TPR)-containing, alpha 339 9627 SNCAIP synuclein, alpha 5 x interactingprotein 340 9552 SPAG7 sperm associated 6 SLE antigen 7 vs RA 341 57522SRGAP1 SLIT-ROBO Rho 6 SLE GTPase activating vs protein 1 RA 342 6744SSFA2 sperm specific 6 SLE antigen 2 vs RA 343 6487 ST3GAL3 ST3 beta- 6SLE galactoside alpa- vs 2,3- RA sialyltransferase 3 344 23345 SYNE1spectrin repeat 6 SLE containing, nuclear vs envelope 1 AID 345 6879TAF7 TAF7 RNA polymerase 6 SLE II, TATA box vs binding protein HV(TBF)-associated factor, 55 kDa 346 6895 TARBP2 TAR (HIV-1) RNA 6 SLEbinding protein 2 vs RA 347 6949 TCOF1 Treacher Collins- 6 SLEFranceschetti vs syndrome 1 RA 348 7980 TFPI2 tissue factor 5 x pathwayinhibitor 2 349 56674 TMEM9B TMEM9 domain 6 SLE family, member B vs RA350 11189 TNRC4 trinucleotide 5 x repeat containing 4 351 10155 TRIM28tripartite motif- 6 SLE containing 28 vs HV 352 7204 TRIO triplefunctional 6 SLE domain (PTPRF vs interacting) RA 353 203068 TUBBtubulin, beta 6 SLE vs RA 354 7280 TUBB2A tubulin, beta 2A SLE vs RA 35527229 TUBGCP4 tubulin, gamma 6 SLE complex associated vs protein 4 RA356 10422 UBAC1 UBA domain 6 SLE containing 1 vs RA 357 7316 UBCubiquitin C 6 SLE vs RA 358 55585 UBE2Q1 ubiquitin- 6 SLE conjugatingenzyme vs E2Q familiy member 1 HV 359 65109 UPF3B UPF3 regulator of 5 xnonsense transcripts homolog B (yeast) 360 7378 UPP1 uridine 6 SLEphosphorylase 1 vs AID 361 64856 VWA1 von Willebrand 6 SLE factor Adomain vs containing 1 RA 362 55884 WSB2 WD repeat and SOCS 5 xbox-containing 2 363 9877 ZC3H11A zinc finger CCCH- 5 x type containing11A 364 55854 ZC3H15 zinc finger CCCH- 6 SLE type containing 15 vs HV365 7592 ZNF41 zinc finger protein 6 SLE 41 vs RA 366 170959 ZNF431 zincfinger protein 6 SLE 431 vs RA 367 146542 ZNF688 zinc finger protein 6SLE 688 vs RA 368 4670 HNRNPM heterogeneous 7 SLE nuclear vsribonucleoprotein M HV 369 10540 DCTN2 dynactin 2 (p50) 7 SLE vs HV 37010938 EHD1 EH-domain 7 SLE containing 1 vs HV 371 38 ACAT1Acetyl-Coenzyme A 7 SLE acetyltransferase 1 vs (acetoacetyl HV CoenzymeA thiolase) 372 684 BST2 bone marrow stromal 7 SLE cell antigen 2 vs HV373 1058 CENPA centromere protein A 7 SLE vs HV 374 1665 DHX15 DEAH(Asp-Glu-Ala- 7 SLE His) box polypeptide vs 15 HV 375 3092 HIP1Huntingtin 7 SLE interacting protein vs 1 HV 376 3336 HSPE1 heatingshock 10 kDa 7 SLE protein 1 vs (chaperonin 10) HV 377 5455 POU3F3 POUclass 3 homeobox 7 SLE 3 vs HV 378 5918 RARRES1 retinoic acid 7 SLEreceptor responder vs (tazarotene induced) HV 1 379 6136 RPL12ribosomalprotein L12 7 SLE vs HV 380 6626 SNRPA small nuclear 7 SLEribonucleoprotein vs polypeptide A HV 381 6631 SNRPC small nuclear 7 SLEribonucleoprotein vs polypeptide C HV 382 6757 SSX2 synovial sarcoma, X7 SLE breakpoint 2 vs HV 383 9788 MTSS1 metastasis 7 SLE suppressor 1 vsHV 384 10134 BCAP31 B-cell receptor- 7 SLE associated protein vs 31 HV385 10522 DEAFl deformed epidermal 7 SLE autoregulatory vs factor 1 HV(Drosophila) 386 10633 RASLl0A RAS-like, family 10, 7 SLE member A vs HV387 54795 TRPM4 transient receptor 7 SLE potential cation vs channel,subfamily HV M, member 4 388 54913 RPP25 ribonuclease P/MRP 7 SLE 25 kDasubunit vs HV 389 54994 C20orf11 chromosome 20 open 7 SLE reading frame11 vs HV 390 55727 BTBD7 BTB (POZ) domain 7 SLE containing 7 vs HV 39179140 CCDC28B coiled-coil domain 7 SLE containing 28B vs HV 392 79613TMCO7 transmembrane and 7 SLE coiled-coil domains vs 7 HV 393 5504PPP1R2 protein phosphatase 7 SLE 1, regulatory vs (inhibitor subunit 2HV 394 8349 HIST2H2BE histone cluster 2, 7 SLE H2be vs HV 395 11168PSIPl PC4 and SFRS1 7 SLE interacting protein vs 1 HV 396 149986 LSM14BLSM14B, SCD6 homolog 7 SLE B (S. cerevisiae) vs HV 397 655 BMP7 Bonemorphogenetic 7 SLE protein 7 vs (osteogenic protein HV 1) 398 1676 DFFADNA fragmentation 7 SLE factor, 45 kDa, alpha vs polypeptide HV 399 3071NCKAPlL NCK-associated 7 SLE protein 1-like vs HV 400 3727 JUND jun Dproto-oncogene 7 SLE vs HV 401 3960 LGALS4 lectin, galactoside- 7 SLEbinding, soluble, 4 vs HV 402 4920 ROR2 Receptor tyrosine 7 SLEkinase-like orphan vs receptor 2 HV 403 7424 VEGFC vascular endothelial7 SLE growth factor C vs HV 404 8906 AP1G2 adaptor-related 7 SLE proteincomplex 1, vs gamma 2 subunit HV 405 10297 APC2 adenomatosis 7 SLEpolyposis coli 2 vs HV 406 10841 FTCD Formiminotransferase 7 SLEcyclodeaminase vs HV 407 11066 SNRNP35 small nuclear 7 SLEribonucleoprotein vs 35 kDa (Ull/U12) HV 408 11345 GABARAPL2GABA(A)receptor- 7 SLE associated protein- vs like 2 HV 409 25854FAM149A family with sequence 7 SLE similarity 149, vs member A HV 41026065 LSM14A LSM14A, SCD6 homolog 7 SLE A (S. cerevisiae) vs HV 41128998 MRPL13 mitochondrial 7 SLE ribosomal protein vs L13 HV 412 51520LARS leucyl-tRNA 7 SLE systhetase vs HV 413 55747 FAM21B family withsequence 7 SLE similarity 21, vs member B HV 414 64841 GNPNAT1glucosamine- 7 SLE phosphate N- vs acetyltransferase 1 HV 415 83483PLVAP Plasmalemma vesicle 7 SLE associated protein vs HV 416 84968PNMA6A paraneoplastic 7 SLE antigen like 6A vs HV 417 118430 MUCLlMucin-like 1 7 SLE vs HV 418 122830 NAT12 N-acetyltransferase 7 SLE 12vs HV 419 221092 HNRNPUL2 heterogeneous 7 SLE nuclear vsribonucleoprotein U- HV like 2 420 388962 BOLA3 bolA homolog 3 7 SLE (E.coli) vs HV 421 729230 FLJ78302 Similar to c-c 7 SLE chemokine receptorvs type 2 (C-C CKR-2) HV (CC-CKR-2) (CCR-2) (CCR2) (Monocytechemoattractant protein 1 receptor) (MCP-1-R) (CD192 antigen) 422 729447GAGE2A G antigen 2A 7 SLE vs HV 423 1152 CKB No Gene Name; 7 SLEcreatine kinase, vs brain HV 424 972 CD74 CD74 molecule, major 7 SLEhistocompatibility vs complex, class II HV invariant chain 425 1397CRIP2 cysteine-rich 7 SLE protein 2 vs HV 426 2040 STOM stomatin 7 SLEvs HV 427 2316 FLNA filamin A, alpha 7 SLE vs HV 428 4000 LMNA lamin A/C7 SLE vs HV 429 4582 MUCl mucin 1, cell 7 SLE surface associated vs HV430 5230 PGKl Phosphoglycerate 7 SLE kinase 1 vs HV 431 5340 PLGplasminogen 7 SLE vs HV 432 6525 SMTN smoothelin 7 SLE vs HV 433 8936WASFl WAS protein family, 7 SLE member 1 vs HV 434 23647 ARFIP2ADP-ribosylation 7 SLE factor interacting vs protein 2 HV 435 6712SPTBN2 spectrin, beta, non- 7 SLE erythrocytic 2 vs HV 436 6729 SRP54signal recognition 7 SLE particle 54 kDa vs HV 437 9987 HNRPDLheterogeneous 7 SLE nuclear vs ribonucleoprotein D- HV like 438 337APOA4 Apolipoprotein A-IV 7 SLE vs HV 439 950 SCARB2 scavenger receptorclass B, member 2 440 3183 HNRNPC heterogeneous 7 SLE nuclear vsribonucleoprotein C HV (Cl/C2) 441 3185 HNRPF Heterogeneous 7 SLEnuclear vs ribonucleoprotein F HV 442 3313 HSPA9 heat shock 70 kDa 7 SLEprotein 9 (mortalin) vs HV 443 3467 IFNWl Interferon, omega 1 7 SLE vsHV 444 3799 KIF5B kinesin family 7 SLE member 5B vs HV 445 7918 BAT4HLA-B associated 7 SLE transcript 4 vs HV 446 8337 HIST2H2AA3 histonecluster 2, 7 SLE H2aa3 vs HV 447 10195 ALG3 asparagine-linked 7 SLEglycosylation 3, vs alpha-1,3- HV mannosyltransferase homolog (S.cerevisiae) 448 23299 BICD2 bicaudal D homolog 2 7 SLE (Drosophila) vsHV 449 80184 CEP290 centrosomal protein 7 SLE 290 kDa vs HV 450 90861HNlL hematological and 7 SLE neurological vs expressed 1-like HV 451349136 WDR86 WD repeat domain 86 7 SLE vs HV 452 no Gene ID dsDNA dsDNA7 SLE vs HV 453 60 ACTB actin, beta 8 SLE vs HV 454 498 ATP4A1 ATPsynthase, H+ 8 SLE transporting, vs mitochondrial Fl HV complex, alphasubunit 1, cardiac muscle 455 506 ATP5B ATP synthase, H+ 8 SLEtransporting, vs mitochondrial Fl HV complex, beta polypeptide 456 563AZGPl alpha-2- 8 SLE glycoprotein 1, vs zinc-binding HV 457 602 BCL3B-cell CLL/lymphoma 8 SLE 3 vs HV 458 1729 DIAPHl diaphanous-related 8SLE formin 1 vs HV 459 1937 EEFlG eukaryotic 8 SLE translation vselongation factor 1 HV gamma 460 1973 EIF4Al eukaryotic 8 SLEtranslation vs initiation factor HV 4A1 461 2280 FKBPlA FK506 binding 8SLE protein lA, 12 kDa vs HV 462 2495 FTHl ferritin, heavy 8 SLEpolypeptide 1 vs HV 463 2597 GAPDH glyceraldehyde-3- 8 SLE phosphate vsdehydrogenase HV 464 2819 GPDl glycerol-3- 8 SLE phosphate vsdehydrogenase 1 HV (soluble) 465 3295 HSD17B4 hydroxysteroid 17- 8 SLEbeta) dehydrogenase vs 4 HV 466 3305 HSPAlL heat shock 70 kDa 8 SLEprotein 1-like vs HV 467 3312 HSPA8 heat shock 70 kDa 8 SLE protein 8 vsHV 468 4174 MCM5 minichromosome 8 SLE maintenance complex vs component 5HV 469 4215 MAP3K3 mitogen-activated 8 SLE protein kinase vs kinasekinase 3 HV 470 4591 TRIM37 tripartite motif 8 SLE containing 37 vs HV471 4691 NCL nucleolin 8 SLE vs HV 472 4898 NRDl nardilysin (N- 8 SLEarginine dibasic vs convertase) HV 473 4904 YBXl Y box binding 8 SLEprotein 1 vs HV 474 5037 PEBPl phosphatidylethanol 8 SLE amine bindingvs protein 1 HV 475 5315 PKM2 pyruvate kinase, 8 SLE muscle vs HV 4765481 PPID peptidylprolyl 8 SLE isomerase D vs HV 477 5684 PSMA3proteasome 8 SLE (prosome, vs macropain)subunit, HV alpha type, 3 4786128 RPL6 ribosomal protein L6 8 SLE vs HV 479 6129 RPL7 ribosomalprotein L7 8 SLE vs HV 480 6130 RPL7A ribosomal protein 8 SLE L7a vs HV481 6132 RPL8 ribosomal protein LB 8 SLE vs HV 482 6187 RPS2 ribosomalprotein S2 8 SLE vs HV 483 6189 RPS3A ribosomal protein 8 SLE S3A vs HV484 6249 CLIPl CAP-GLY domain 8 SLE containing linker vs protein 1 HV485 6793 STKl0 serine/threonine 8 SLE kinase 10 vs HV 486 6880 TAF9 TAF9RNA polymerase 8 SLE II, TATA box binding vs protein (TBP)- HVassociated factor, 32 kDa 487 7001 PRDX2 peroxiredoxin 2 8 SLE vs HV 4887552 ZNF711 zinc finger protein 8 SLE 711 vs HV 489 8260 ARDlA N(alpha)-8 SLE acetyltransferase vs 10, NatA catalytic HV subunit 490 8317 CDC7cell division cycle 8 SLE 7 vs HV 491 8667 EIF3H eukaryotic 8 SLEtranslation vs initiation factor HV subunit H 492 9223 MAGil membraneassociated 8 SLE guanylate kinase, WW vs and PDZ domain HV containing 1493 9230 RABllB RABllB, member RAS 8 SLE oncogene family vs HV 494 9425CDYL chromodomain 8 SLE protein, Y-like vs HV 495 9694 EMC2 ER membraneprotein 8 SLE complex subunit 2 vs HV 496 10075 HUWEl HECT, UBA and WWE8 SLE domain containing 1, vs E3 ubiquitin protein HV ligase 497 10109ARPC2 actin related 8 SLE protein 2/3 complex, vs subunit 2, 34 kDa HV498 10180 RBM6 RNA binding motif 8 SLE protein 6 vs HV 499 10273 STUBlSTIPl homology and 8 SLE U-box containing vs protein 1, E3 HV ubiquitinprotein ligase 500 10432 RBM14 RNA binding motif 8 SLE protein 14 vs HV501 10539 GLRX3 glutaredoxin 3 8 SLE vs HV 502 10806 SDCCAG8serologically 8 SLE defined colon cancer vs antigen 8 HV 503 11108 PRDM4PR domain containing 8 SLE 4 vs HV 504 23002 DAAMl dishevelled 8 SLEassociated activator vs of morphogenesis 1 HV 505 23351 KHNYN KH and NYNdomain 8 SLE containing vs HV 506 23589 CARHSP1 calcium regulated 8 SLEheat stable protein vs 1, 24 kDa HV 507 26986 PABPCl poly (A) binding 8SLE protein, cytoplasmic vs 1 HV 508 27072 VPS41 vacuolar protein 8 SLEsorting 41 homolog vs (S. cerevisiae) HV 509 30836 DNTTIP2deoxynucleotidyltransferase, 8 SLE terminal, vs interacting protein HV 2510 51028 VPS36 vacuolar protein 8 SLE sorting 36 homolog vs (S.cerevisiae) HV 511 51082 POLRlD polymerase (RNA) I 8 SLE polypeptide D,16 kDa vs HV 512 51138 COPS4 COP9 signalosome 8 SLE subunit 4 vs HV 51351466 EVL Enah/Vasp-like 8 SLE vs HV 514 54869 EPS8Ll EPS8-like 1 8 SLEvs HV 515 54903 MKSl Meckel syndrome, 8 SLE type 1 vs HV 516 57017 COQ9coenzyme Q9 8 SLE vs HV 517 57026 PDXP pyridoxal 8 SLE (pyridoxine,vitamin vs B6) phosphatase HV 518 57221 ARFGEF3 ARFGEF family 8 SLEmember 3 vs HV 519 64753 CCDC136 coiled-coil domain 8 SLE containing 136vs HV 520 80208 SPGll spastic paraplegia 8 SLE 11 (autosomal vsrecessive) HV 521 83858 ATAD3B ATPase family, AAA 8 SLE domaincontaining 3B vs HV 522 84893 FBXO18 F-box protein, 8 SLE helicase, 18vs HV 523 129563 DIS3L2 DIS3 like 3′-5′ 8 SLE exoribonuclease 2 vs HV524 144097 Cllorf84 chromosome 11 open 8 SLE reading frame 84 vs HV 525256364 EML3 echinorm microtubule 8 SLE associated protein vs like 3 HV526 347733 TUBB2B tubulin, beta 2B 8 SLE class IIb vs HV 527 3303 HSPAlAheat shock 70 kDa 8 SLE protein 1A vs HV 528 5163 PDKl pyruvate 8 SLEdehydrogenase vs kinase, isozyme 1 HV 529 1001 CDH3 cadherin 3, type 1,8 SLE P-cadherin vs (placental) HV

Example 9: Identification of Autoantibody Reactivities in ENA-4-NegativeSLE Patients

In order to identify new SLE-specific autoantigens, the autoantibodyprofiles of new SLE-specific autoantigens were the autoantibody profilesof the group of SLE patients seropositive for the autoantigensSm-protein, U1-RNP, Rho52/SS-A and Ro60/SS-B, with which theseronegative was compared. The result of the statistical test issummarised in Table 2.

Group 4 comprises additional antigens suitable for the identification ofENA-4-negative SLE patients.

FIG. 5 shows the volcano plot of the autoantibody reactivities ofENA-4-positives compared to ENA-4-negative SLE patients.

Example 10: Calculation of Antigen Panels for Improved Diagnosis of SLE

Due to the high clinical and serological heterogeneity of the SLEdisease, it is not possible to diagnose this disease using just onebiomarker. It is therefore necessary to combine (where possible)uncorrelated biomarker panels to form what are known as biomarkerpanels.

Group 1 of the antigens in Table 2 comprises the most important 24antigens used for the calculation of biomarker panels for the diagnosisof SLE.

Table 4 shows different combinations of antigens which were used for thecalculation of the biomarker panels (ENA-4, ENA-4+anti-rib, PI, PII,PIII, PVI, PV).

FIG. 6 shows the sensitivity and specificity and also the area under thecurve (AUC) for the known 4 antigens compared with antigen panels thatwere calculated using a combination of the antigens from Table 2. Due tothe inclusion of the 3 ribosomal antigens anti-rib) RPLP0, RPLP1 andRPLP2, the sensitivity could be increased already by 10% compared withthe known 4 ENA antigens from 0.63 to 0.72. However, only a freelyselected combination of known and new antigens could increase thesensitivity by 20% compared with the ENA-4 test to 0.8.

Antigens which have an adjusted p-value for the non-parametric meanvalue comparison between groups of <0.05, alongside a fold changeof >1.5 and additionally an AUC resulting from the ROC analysis of >0.75were selected on the basis of the univariate results for the generationof panels. In addition, the ENA-4 antigens were selected. For this poolof selected candidates, an L1-penalised logistic regression model wasestablished within the scope of a nested cross validation. Antigenswhich were not taken into consideration within the scope of the modelformation were removed from the further consideration. Within theremaining pools, panel contents were defined, for example in accordancewith established markers and new markers.

Group 4 in Table 2 contains further statistically significant antigenswhich can be used for the identification of ENA-4-negative patients andfor the definition of biomarker panels.

Group 6 in Table 2 contains further statistically significant antigenswhich can be used for the diagnosis and differential diagnosis of SLEcompared with healthy controls and other autoimmune diseases.

TABLE 4 Composition of the diagnostic SLE Panel Panels ENA-4 + GeneSymbol Gene Name Antigen ENA-4 anti-rib PI PII PIII PVI PV SNRPN smallnuclear Sm X X X X SEQ ID ribonucleoprotein protein D NO. 14 polypeptideN TRIM 21 tripartite motif- SSA/RO X X X X X SEQ ID containing 21 NO. 19TROVE2 TROVE domain SSA/Ro60 X X X X X SEQ ID family, member 2 NO. 20SSB Sjogren sindrome SSB/La X X X X X SEQ ID antigen B NO. 17(autoantigen La) SNRNP70 small nuclear Ul-RNP X X X X X SEQ IDribonucleoprotein NO. 12 70 kDa (Ul) SNRPB small nuclear Sm X X X X XSEQ ID ribonucleoprotein protein NO. 13 polypeptides B B/B′ and Bl RPLP0ribosomal anti-rib X X X X SEQ ID protein, large, NO. 8 PO RPLP2ribosomal anti-rib X X X SEQ ID protein, large, NO. 10 P2 RPLPlribosomal anti-rib X X X SEQ ID protein, large, NO. 9 Pl XRCCS X-rayrepair Ku80 X SEQ ID complementing NO. 22 defective repair in Chinesehamster cells 5 (double-strand- break rejoining) VIM vimentin X X SEQ IDNO. 21 SPTB spectrin, beta, X X SEQ ID erythrocytic NO. 16 DBTdihydrolipoamide X X X X X SEQ ID branched chain NO. 1 transacylase E2EZR ezrin X X X X X SEQ ID NO. 3 HNRNPA2B1 heterogeneous X X SEQ IDnuclear NO. 6 ribonucleoprotein A2/B1 TMPO thymopoietin X X X X SEQ IDNO. 18 MVP major vault X X X X SEQ ID protein NO. 7 ZNF574 zinc finger XX X SEQ ID protein 574 NO. 24 HIST1H2BD histone cluster anti- X X SEQ ID1, H2bd histone NO. 4 SH3KBP1 SH3-domain kinase X SEQ ID binding protein1 NO. 11 ZNF217 zinc finger X X SEQ ID protein 217 NO. 23 SPl00 SPl00nuclear X X X X X SEQ ID antigen NO. 15 HNRNPAl heterogeneous X X X X XSEQ ID nuclear NO. 5 ribonucleoprotein Al DLAT dihydrolipoamide PDC-E2,M2 X X X X SEQ ID S-acetyltransferase antigen NO. 2

TABLE 5 AUC, sensitivity and specificity of the SLE panels SLE vs PSSAUC Cl (AUC) Sans. Cl (Sens.) Spec. Cl (Spec) a) SLE versus healthycontrols Panel PI 0.99 [0.94, 0.98] 0.83 [0.77, 0.9]  0.98 [0.96, 1.0] Panel PII 0.90 [0.84, 0.95] 0.63 [0.53, 0.73] 0.94 [0.91, 0.98] PanelPIII 0.91 [0.87, 0.95] 0.61  [0.5, 0.72] 0.95 [0.92, 0.98] Panel PIV0.90 [0.86, 0.94] 0.57 [0.44, 0.71] 0.95 [0.91, 0.99] Panel PV 0.91[0.87, 0.96] 0.64 [0.52, 0.76] 0.95 [0.91, 0.99] ENA-4 0.89 [0.84, 0.94]0.63 [0.49, 0.77] 0.96  [0.9, 0.98] ENA-4 + 0.93 [0.88, 0.98] 0.72 [0.6, 0.84] 0.97 [0.95, 0.99] anti-rib b) SLE versus SSc (PSS) Panel PI0.9 [0.85, 0.95] 0.78 [0.73, 0.83] 0.83 [0.71, 0.94] Panel PII 0.83[0.78, 0.88] 0.72 [0.61, 0.83] 0.76 [0.98, 0.85] Panel PIII 0.81 [0.74,0.88] 0.68 [0.56, 0.79] 0.75  [0.6, 0.89] Panel PIV 0.83 [0.78, 0.88]0.69 [0.58, 0.81] 0.77 [0.67, 0.88] Panel PV 0.84 [0.79, 0.9]  0.71[0.62, 0.8]  0.76 [0.65, 0.87] ENA-4 0.75 [0.66, 0.85] 0.6 [0.5, 0.7]0.8 [0.71, 0.88] ENA-4 + 0.82 [0.74, 0.9]  0.63 [0.51, 0.75] 0.83 [0.74,0.93] anti-rib c) SLE versus all AID (early RA, SSc, SPA) SLE vs Pool(EA, PSS, SPA) AUC Cl (AUC) Sans. Cl (Sens.) Spec. Cl (Spec) Panel PI0.94 [0.91, 0.96] 0.6 [0.51, 0.69] 0.98 [0.98, 0.99] Panel PII 0.83[0.78, 0.89] 0.26 [0.16, 0.35] 0.98 [0.97, 0.99] Panel PIII 0.83 [0.74,0.92] 0.27 [0.16, 0.37] 0.99 [0.98, 1]   Panel PIV 0.83 [0.79, 0.87]0.19 [0.1, 0.28] 0.98 [0.97, 0.99] Panel PV 0.85 [0.78, 0.91] 0.34[0.22, 0.46] 0.99 [0.98, 0.99] ENA-4 0.84 [0.79, 0.9]  0.35 [0.22, 0.47]0.99 [0.98, 0.99] ENA-4 + 0.91 [0.88, 0.93] 0.49 [0.41, 0.58] 0.98[0.97, 0.99] anti-rib

Example 11: Identification of lupus nephritis patients

The autoantibody profiles of SLE patients with lupus nephritis werecompared with those of SLE patients without lupus nephritis. Followingunivariate statistical evaluation, a threshold value of p<0.05 and a 1.5times modified reactivity compared with the control group were applied.85 antigens met these criteria and are detailed in Table 2.

FIG. 7 shows the volcano plot of the sera compared with selected lupusnephritis antigens.

Group 2 in Table 2 contains 30 additional and important antigens whichcan be used for the generation of lupus nephritis biomarker panels.

An L1-penalised logistic regression model with five-fold crossvalidation and twenty times repetition was computed for the selection ofthe best candidates. The antigens selected most frequently in this modelcomputation with a frequency of more than 50% constituted the bestcandidates for the diagnosis of lupus nephritis.

FIG. 8 shows the frequency distribution of the lupus nephritis antigens.

Group 5 comprises further statistically significant antigens suitablefor the diagnosis of lupus nephritis.

Example 12: Identification of SLE subforms and subgroups

The large clinical heterogeneity of SLE constitutes a big problem bothfor diagnosis and active substance development.

The identification of specific antibody signatures in SLE patientsubgroups thus constitutes a key step for the improved definition ofpatient groups in clinical studies. By way of example, as presentedunder Example 9, specific antibodies for lupus nephritis could be usedto recruit this subgroup for drug studies.

A large number of new active substances and therapeutic antibodies arecurrently undergoing clinical development: inter alia, therapeuticantibodies against cell-surface receptors of immune cells, such asanti-CD20, anti-CD22, or against pro-inflammatory cytokines, such asanti-IL6, are being developed. It is therefore now possible, due to theidentification of serologically-defined subgroups of SLE, to link thisto a target-specific response to a drug.

It was first examined whether, on the basis of the typical ENA antigensand ribosomal antigens, different autoantibody signatures can already beidentified in SLE patients and thus patient subgroups.

FIGS. 9a and b show a dendogram of the SLE antigens after calculation ofSpearman's rank correlation coefficient

FIG. 9a shows a dendogram for the antigens Sm, SS-B, Ro-52/SS-A,Ro60-SS-B and three ribosomal proteins.

3 antigen clusters can be already be defined on the basis of these 7antigens.

For an improved definition of SLE subgroups, however, a larger number ofantigens are necessary. 50 antigens from Table 2 were thereforeselected, and the correlation thereof in SLE patients was examined bycalculation of Spearman's rank correlation coefficient.

Group 3 contains 37 of the most important antigens necessary for thecharacterisation of SLE subgroups. Further antigens have already beendefined in group 1 and group 2.

The presentation of the antigens as a dendogram shows groups of antigensof which the reactivities in SLE patients are correlated with oneanother.

As illustrated in FIG. 9b , at least 6 groups of correlated antigens canbe identified as a result.

Interestingly, one of the clusters includes the antigens MVP, MIER2,CCS, DCAF6, which were identified in the table as biomarkers for lupusnephritis.

Due to the calculation of a PPLS-DA-based regression model, it ispossible to visualise how well the selected antigens contribute to thediscrimination of the SLE patients from healthy controls.

FIGS. 10a and b show the PPLS-DA biplot of the SLE patients and healthycontrols with use of the SLE antigens.

FIG. 10a shows a PPLS-DA biplot for the selected ENA antigens andribosomal proteins and measured values thereof in the SLE patients. FIG.10a shows that the separation of healthy and SLE is not complete andthat some SLE patients coincide with the group of healthy samples.However, there is already a division of the SLE patients into 2 clusterswith just few antigens.

FIG. 10b shows a PPLS-DA biplot for 50 antigens which are contained inTable 2. The selection of further antigens results in a practicallyperfect separation of the SLE patients and healthy samples.

A further subdivision of the SLE patients into possible subgroups isprovided by 50 antigens. These subgroups can be defined by specificantigens, some of which have been highlighted by way of example.

Example 13: Validation of SLE Antigens in an Independent Test Cohort II

For validation of the SLE-associated autoantigens specified in

Table 2, the autoantibody reactivity in serum samples of a furtherindependent cohort of 101 SLE patients, 105 healthy controls and 89samples of the SLE cohort from Example 6 was measured. For this purposethe 529 human proteins specified in Table 2 (SEQ ID No. 1057 to 1584),and double-stranded DNA (dsDNA) thereof, were coupled to Luminex beads,and the antigen-coupled beads were measured in a multiplex assay withthe patient samples. The binding of autoantibodies was measured by meansof a PE-conjugated autoantibody in a Luminex instrument.

Following univariate statistical evaluation, a threshold value of p<0.05(Wilcoxon rank-sum test) compared with the control group was applied.

A list of the significance values (p-values) for autoantibodies against50 antigens in the SLE cohort II is shown in Table 6. Of the 50antigens, 43 antigens in cohort I and cohort II achieved a p-value<0.05.

The frequency (in %) of autoantibodies against 50 antigens in the threeSLE cohorts is shown in Table 7.

FIG. 11: shows the calculated p-value of the antigens from Table 2 andalso the frequency of SLE patients who were classified asautoantibody-positive for this antigen.

Example 14: Validation of SLE Autoantigens in a Third Independent TestCohort III

For validation of the SLE-associated autoantigens specified in Table 2,the autoantibody reactivity in serum samples of an independent cohort of183 SLE patients and 109 healthy controls was measured. For thispurpose, 6,912 human proteins were coupled to Luminex beads and theprotein-coupled beads were measured in a multiplex assay with thepatient samples. The binding of autoantibodies was measured by means ofa PE-conjugated autoantibody in a Luminex instrument.

After univariate statistical evaluation, a threshold value of p<0.05 anda Cohen's d effect size of greater than 0.3 compared to the controlgroup was provided.

A list of the significance values is shown in Table 6. The tablecontains selected markers which are part of the panels ENA+anti-rib,panel I, panel VI, panel VII and panel VIII. The table contains furthermarkers which achieved a p-value of <0.05 in all three cohorts.

TABLE 6 significance values (p-values) of 50 antigens in 3 SLE cohortsGene SLE SLE SLE Seq. Nr GenID Symbol cohort I cohort II cohort IIIPanel 1 1629 DBT 1.28E−04 2.16E−03 3.82E−03 Panel I; II; III; IV; V; VII2 1737 DLAT 6.33E−08 4.12E−11 1.31E−04 Panel I; III; IV; VI; VII 3 7430EZR 1.44E−03 2.68E−01 9.79E−02 panel I; II; III; IV 4 3017 HIST1H2BD9.43E−03 4.08E−01 4.00E−02 Panel II, V 5 3178 HNRNPA1 1.99E−09 3.60E−062.81E−04 Panel I; II, III; IV; V; VI; VII 6 3181 HNRNPA2B1 7.31E−082.81E−05 1.70E−05 Panel III; V; VI; VII 7 9961 MVP 1.40E−03 3.90E−061.56E−04 Panel I; II; III; V; VI; VII 8 6175 RPLP0 4.59E−13 4.75E−123.51E−08 ENA-4 + anti-rib, Panel I; III; VI; VII 9 6176 RPLP1 4.61E−113.05E−13 7.05E−07 ENA-4 + anti-rib; Pane lIII; IV; VII 10 6181 RPLP22.38E−10 5.18E−10 2.94E−09 ENA-4 + anti-rib; Penal I; VI; VII 11 30011SH3KBP1 1.68E−04 2.22E−08 2.64E−02 Panel V 12 6625 SNRNP70 4.87E−029.02E−02 1.22E−08 ENA-4 + anti-rib; Panel I; II; IV 13 6628 SNRPB2.95E−09 5.57E−07 2.49E−09 ENA-4 + anti-rib; Panel I; II; IV; VI; VII 146638 SNRPN 7.44E−05 2.61E−02 3.64E−02 EN-4 + anti-rib, Panel II; PanelIV 15 6672 SP100 1.98E−04 2.47E−04 3.04E−07 Panel I; II; III; IV; V; VII16 6710 SPTB 7.76E−06 5.13E−01 8.37E−01 Panel III; V 17 6741 SSB1.75E−03 3.20E−02 7.82E−02 ENA-4 + anti-rib; Panel I; II; IV 18 7112TMPO 2.20E−03 3.15E−02 1.15E−05 Panel I; II; III; IV; VI 19 6737 TRIM215.07E−12 1.96E−10 6.35E−10 Panel I; II; iV; VI; VII 20 6738 TROVE26.11E−04 2.59E−01 9.27E−05 ENA-4 + anti-rib; Panel I; II; IV 21 7431 VIM2.73E−01 2.25E−04 1.06E−03 Panel III; V 22 7520 XRCC5 2.06E−06 2.01E−057.83E−04 Panel V; VI; VII 23 7764 ZNF217 3.28E−01 1.55E−01 5.04E−05Panel III; V 24 64763 ZNF574 1.02E−02 8.36E−04 1.33E−03 Panel I; II; V;VII 31 9973 CCS 6.65E−06 5.28E−06 6.62E−09 Panel VII 95 6629 SNRPB21.06E−03 8.68E−03 3.66E−06 Panel VIII 128 10970 CKAP4 1.52E−05 7.26E−084.60E−05 Panel VIII 134 1743 DLST 1.63E−05 1.78E−06 4.95E−05 Panel VII168 4841 NONO 1.27E−04 3.76E−07 5.17E−04 Panel VI; VII 169 29982 NRBF22.22E−04 2.44E−02 7.44−03 Panel VIII 171 4926 NUMA1 1.62E−03 4.28E−054.31−03 Panel VIII 214 7791 ZYX 4.54E−04 1.77E−05 2.57E−03 Panel VII 3684670 HNRNPM 7.61E−03 8.98E−03 2.34E−05 Panel VII 369 10540 DCTN21.11E−06 1.69E−08 2.49E−05 Panel VII 370 10938 EHD1 5.60E−05 1.73E−051.01E−03 Panel VII 372 684 BST2  251E−02 1.44E−02 1.13E−08 Panel VIII373 1058 CENPA 4.45E−04 8.70E−06 2.51E−05 Panel VIII 375 3092 HIP14.42E−02 8.73E−07 2.03E−04 Panel VIII 376 3336 HSPE1 2.15E−02 1.42E−021.73E−03 Panel VIII 377 5455 POU3F3 1.31E−03 1.02E−04 6.18E−03 PanelVIII 380 6626 SNRPA 7.16E−12 1.85E−11 2.60E−16 Panel VIII 381 6631 SNRPC1.42E−06 1.06E−07 3.73E−15 Panel VIII 382 6757 SSX2 2.40E−03 1.78E−022.09E−04 Panel VIII 384 10134 BCAP31 4.10E−02 1.04E−05 4.34E−08 PanelVIII 390 55727 BTBD7 3.33E−02 3.68E−04 1.79E−04 Panel VIII 428 4000 LMNA1.59E−03 7.49E−04 3.41E−04 Panel VIII 429 4582 MUC1 1.35E−04 1.66E−056.29E−04 Panel VIII 431 5340 PLG 1.22E−03 1.64E−02 5.61E−03 Panel VIII432 6525 SMTN 2.05E−03 1.53E−02 9.78E−03 Panel VIII 452 dsDNA dsDNA1.65E−06 5.35E−17 NA dsDNA

TABLE 7 List of the frequency of SLE patients positively tested forautoantibodies in 3 independent cohorts. The frequency in % ofindividuals positively tested for autoantibodies from Table 6 wascalculated by means of the 95% quantile of healthy controls. Proportionof SLE patients positively tested for autoantibodies (%) based on the95% quantile of the control group Seq. Gene SLE SLE SLE Nr. GeneIDSymbol cohort I cohort II cohort III Panel 1 1629 DBT 1.28E−04 2.16E−033.82E−03 Panel I: II; III; IV; V; VII 2 1737 DLAT 6.33E−08 4.12E−111.31E−04 Panel I; III; IV; VI; VII 3 7430 EZR 1.44E−03 2.68E−01 9.79E−02panel I; II; III; IV 4 3017 HIST1H2BD 9.43E−01 4.08E−01 4.00E−01 PanelII, V 5 3178 HNRNPA1 1.99E−09 3.60E−06 2.81E−04 Panel I; II, III; IV; V;VI; VII 6 3181 HNRNPA2B1 7.31E−08 2.81E−05 1.70E−05 Panel III; V; VI;VII 7 9961 MVP 1.40E−03 3.90E−06 1.56E−04 Panel I; II; III; V; VI; VII 86175 RPLP0 4.59E−13 4.75E−12 3.51E−08 ENA-4 + anti-rib, Panel I; III;VI; VII 9 6176 RPLP1 4.61E−11 3.05E−13 7.50E−07 ENA-4 + anti-rib; Pane1III; IV; VII 10 6181 RPLP2 2.38E−10 5.18E−10 2.94E−09 ENA-4 + anti-rib;Panel I; VI; VII 11 30011 SH3KBP1 1.68E−04 2.22E−08 2.64E−02 Panel V 126625 SNRNP70 4.87E−02 9.02E−02 1.22E−08 ENA-4 + anti-rib; Panel I; II;IV 13 6628 SNRPB 2.95E−09 5.57E−07 2.49E−09 ENA-4 + anti-rib; Panel I;II; IV; VI; VII 14 6638 SNRPN 7.44E−05 2.61E−02 3.64E−02 ENA-4 +anti-rib, Panel II; Panel IV 15 6672 SP100 1.98E−04 2.47E−04 3.04E−07Panel I; II; III; IV; V; VII 16 6710 SPTB 7.76E−06 5.13E−01 8.37E−01Panel III; V 17 6741 SSB 1.75E−03 3.20E−02 7.82E−02 ENA-4 + anti-rib;Panel I; II; IV 18 7112 TMPO 2.20E−03 3.15E−02 1.15E−05 Panel I; II;III; IV; VI 19 6737 TRIM21 5.07E−12 1.96E−10 6.35E−10 Panel I; II; iV;VI; VII 20 6738 TROVE2 6.11E−04 2.59E−01 9.27E−05 ENA-4 + anti-rib;Panel I; II; IV 21 7431 VIM 2.37E−01 2.25E−04 1.06E−03 Panel III; V 227520 XRCC5 2.06E−06 2.01E−05 7.83E−04 Panel V; VI; VII 23 7764 ZNF2173.28E−01 1.55E−01 5.04E−05 Panel III; V 24 64763 ZNF574 1.02E−028.36E−04 1.33E−03 Panel I; II; V; VII 31 9973 COS 6.65E−06 5.28E−066.62E−09 Panel VII 95 6629 SNRPB2 1.06E−03 8.68E−03 3.66E−06 Panel VIII128 10970 CKAP4 1.52E−05 7.26E−08 4.60E−05 Panel VIII 134 1743 DLST1.63E−05 1.78E−06 4.95E−05 Panel VII 168 4841 NONO 1.27E−04 3.76E−075.17E−04 Panel VI; VII 169 29982 NRBF2 2.22E−04 2.44E−02 7.44E−03 PanelVIII 171 4926 NUMA1 1.62E−03 4.28E−05 4.31E−03 Panel VIII 214 7791 ZYX4.54E−04 1.77E−05 2.57E−03 Panel VII 368 4670 HNRNPM 7.61E−03 8.98E−032.34E−05 Panel VII 369 10540 DCTN2 1.11E−06 1.69E−08 2.49E−05 Panel VII370 10938 EHD1 5.60E−05 1.73E−05 1.01E−03 Panel VII 372 684 BST22.51E−02 1.44E−02 1.13E−08 Panel VIII 373 1058 CENPA 4.45E−04 8.70E−062.51E−05 Panel VIII 375 3092 HIP1 4.42E−02 8.73E−07 2.03E−04 Panel VIII376 3336 HSPE1 2.15e−02 1.42E−02 1.73E−03 Panel VIII 377 5455 POU3F31.31E−03 1.02E−04 6.18E−03 Panel VIII 380 6626 SNRPA 7.16E−12 1.85E−112.60E−16 Panel VIII 381 6631 SNRPC 1.42E−06 1.06E−07 3.73E−15 Panel VIII382 6757 SSX2 2.40E−03 1.78E−02 2.09E−04 Panel VIII 384 10134 BCAP314.10E−02 1.04E−05 4.34E−08 Panel VIII 390 55727 BTBD7 3.33E−02 3.68E−041.79E−04 Panel VIII 428 4000 LMNA 1.59E−03 7.49E−04 3.41E−04 Panel VIII429 4582 MUC1 1.35E−04 1.66E−05 6.29E−04 Panel VIII 431 5340 PLG1.22E−03 1.64E−02 5.61E−03 Panel VIII 432 6525 SMTN 2.05E−03 1.53E−029.78E−03 Panel VIII 452 dsDNA dsDNA 1.65E−06 5.35E−17 NA dsDNA

Example: Calculation of Biomarker Panels

As shown in Table 7, only at most approximately 60% of the SLE patientshad antibodies for a specific autoantigen. In order to thereforeincrease the sensitivity of the diagnostic autoantibodies, such asanti-dsDNA, SSA-Ro (TRIM21/TROVE2) and U1-RNP (SNRNP70, SNRPNA, SNRNPC),new methods with which autoantibodies can be combined to form what areknown as biomarker panels were tested.

For this pool of selected candidates, a logistic regression was carriedout for panels PI to PVII. An L1-penalised logistic regression model wasestablished within the scope of a nested cross validation for panelsPVIII to PXI. Antigens which were not considered within the scope of themodel formation were removed from the further consideration. The contentof panels was defined within the remaining pool, for example inaccordance with established markers and new markers.

The antigens specified in Table 2 were used for the calculation ofbiomarker panels for the diagnosis of SLE.

Table 4 shows different combinations of antigens which were used for thecalculation of the biomarker panels (ENA-4, ENA-4+anti-rib, PI, PII,PIII, PVI, PV).

Table 8 shows further different combinations of antigens which were usedfor the calculation of panels and which were selected on account oftheir significance and reactivity in three SLE cohorts.

TABLE 8 Combinations of antigens from Table 2: Seq. ID Gene Panel +antiPanel Panel Panel Panel Panel Panel Panel Panel Panel Panel Panel NrGeneID Symbol ENA-4 rib PI PII III PIV V VI VII VIII IX X * XI * 1 1629DBT x x x x x x x x x x 2 1737 DLAT x x x x x x x x x x 5 3178 HNRNPAl xx x x x x x x x x x 6 3181 HNRNPA2Bl x x x x x x x x 7 9961 MVP x x x xx x x x x x 8 6175 RPLP0 x x x x x x x x x x 9 6176 RPLPl x x x x x x xx 10 6181 RPLP2 x x x x x x x x x x 13 6628 SNRPB x x x x x x x x x x x15 6672 SP100 x x x x x x x x x x 19 6737 TRIM21 x x x x x x x x x x x22 7520 XRCC5 x x x x x x x 24 64763 ZNF574 x x x x x x x x 134 1743DLST x x x x x 168 4841 NONO x x x x x x 214 7791 ZYX x x x x x 368 4670HNRNPM x x x x x 369 10540 DCTN2 x x x x x 370 10938 EHD1 x x x x x 43017 HIST1H2BD x x x x x x 12 6625 SNRNP70 x x x x x x x x x 17 6741 SSBx x x x x x x x x 18 7112 TMPO x x x x x x x x x x 20 6738 TROVE2 x x xx x x x x x 21 7431 VIM x x x x x x 23 7764 2NF217 x x x x x 29 9478CABP1 x x x x 31 9973 CCS x x x x 46 4869 NPM1 x x x x 95 6629 SNRPB2 xx x x 128 10970 CKAP4 x x x x 136 51143 DYNC1LI1 x x x x 143 23360 FNBP4x x x x 163 4688 NCF2 x x x x 169 29982 NRBF2 x x x x 171 4926 NUMA1 x xx x 188 644096 SDHAF1 x x x x 349 56674 TMEM9B x x x x 371 38 ACAT1 x xx x 372 684 BST2 x x x x 373 1058 CENPA x x x x 374 1665 DHX15 x x x x375 3092 HIP1 x x x x 376 3336 HSPE1 x x x x 377 5455 POU3F3 x x x x 3785913 RARRES1 x x x x 379 6136 RFL12 x x x x 380 6626 SNRPA x x x x 3816631 SNRPC x x x x 382 6757 SSX2 x x x x 383 9788 MTSS1 x x x x 38410134 BCAP31 x x x x 385 10522 DEAF1 x x x x 386 10633 RASL10A x x x x387 54795 TRPM4 x x x x 388 54913 RPP25 x x x x 389 54994 C20orf11 x x xx 390 55727 BTBD7 x x x x 391 79140 CCDC28B x x x x 392 79613 TMCO7 x xx x 424 972 CD74 x x x x 425 1397 CRPI2 x x x x 426 2040 STOM x x x x427 2316 FLNA x x x x 428 4000 LMNA x x x x 429 4582 MUC1 x x x x 4305230 PGK1 x x x x 431 5340 PLG x x x x 432 6525 SMTN x x x x 433 8936WASF1 x x x x 434 23647 ARFIP2 x x x x 3 7430 EXR x x x x x x x x 1130011 SH3KBP1 x x x x 14 6638 SNRPN x x x x x x x 16 6710 SPTB x x x x x33 55802 DCP1A x x x 41 54531 MIER2 x x x 48 11040 PIM2 x x x 74 10933MORF4L1 x x x 105 8615 USO1 x x x 108 375690 WASH5P x x x 114 55256 ADI1x x x 115 9255 AIMP1 x x x 116 54522 ANKRD16 x x x 132 8642 DCHS1 x x x140 100129583 FAM47E x x x 145 64689 GORASP1 x x x 152 23135 KDM6B x x x166 22861 NLRP1 x x x 170 8439 NSMAF x x x 174 5195 PEX14 x x x 186 8578SCARF1 x x x 191 6421 SFPQ x x x 197 54961 SSH3 x x x 203 90326 THAP3 xx x 256 55740 ENAH x x x 264 150946 FAM59B x x x 278 3304 HSPA1B x x x293 4137 MAPT x x x 332 4736 RPL10A x x x 344 23345 SYNE1 x x x 35110155 TRIM28 x x x 359 65109 UPF3B x x x 393 5504 PPP1R2 x x x 394 8349HIST2H2BE x x x 395 11168 PSIP1 x x x 396 149986 LSM14B x x x 435 6712SPTBN2 x x x 436 6729 SRP54 x x x 437 9987 HNRPDL x x x * The panels Xand XI can be supplemented by 20 or more markers from the otheravailable 1587 markers, in particular proteins. Panel VI comprises 11antigens which were measured in all three SLE cohorts with a p-value <0.05. Panel VII comprises 19 antigens which were measured in the threeSLE cohorts with a p-value < 0.05. Panel VIII comprises panel VII and afurther 52 antigens which were found in cohort 3 and at least one of theother SLE cohorts with a p-value < 0.05 for the comparison of SLEagainst healthy controls. Panel IX comprises panel VII, panel VIII and afurther 110 antigens which, in one or two SLE cohorts for the comparisonof SLE against healthy controls, achieved a p-value of 0.05. Panel Xcomprises panel VII, panel VIII, panel IX and a further 227 antigenswhich, as specified in Table 2, originate from different comparisons andachieved a p-value < 0.05 in at least one SLE cohort.

Tables 9a, 9c and 9e show the area under the curve (AUC) confidenceinterval, sensitivity and specificity of different biomarkercombinations in the three different SLE cohorts.

Tables 9b and 9d show the area under the curve (AUC), confidenceinterval, sensitivity and specificity of the different panels in thethree SLE cohorts in combination with anti-dsDNA autoantibodies.

TABLE 9a Area under the curve (AUC), sensitivity and specificity of thedifferent panels in the SLE cohort I. AUC Sensitivity Specificity CohortI lower upper lower upper lower upper Panel mean CI CI mean CI CI meanCI CI PI 0.86 0.84 0.87 0.79 0.76 0.81 0.84 0.82 0.86 PII 0.88 0.87 0.900.81 0.79 0.84 0.82 0.80 0.85 PIII 0.84 0.83 0.86 0.74 0.71 0.76 0.800.77 0.83 PIV 0.85 0.84 0.87 0.80 0.77 0.82 0.83 0.81 0.85 PV 0.81 0.790.83 0.73 0.70 0.75 0.76 0.73 0.79 PVI 0.87 0.86 0.89 0.79 0.77 0.820.83 0.81 0.85 Panel. 0.87 0.85 0.88 0.73 0.71 0.76 0.86 0.84 0.89 ENAPanel. 0.87 0.85 0.88 0.78 0.75 0.80 0.83 0.81 0.85 ENA + antiRib PVII0.79 0.77 0.81 0.75 0.72 0.78 0.77 0.74 0.79 PVIII 0.85 0.83 0.86 0.750.72 0.78 0.82 0.79 0.84 PIX 0.83 0.81 0.84 0.73 0.71 0.76 0.81 0.780.83 PX 0.83 0.81 0.84 0.73 0.70 0.76 0.78 0.76 0.81 PXI 0.83 0.81 0.840.74 0.71 0.76 0.79 0.76 0.81

TABLE 9b Area under the curve (AUC), upper and lower confidence interval(CI), sensitivity and specificity of the biomarker panels in SLE cohortI in combination with anti-dsDNA autoantibodies. Cohort I Panel AUCSensitivity Specificity plus lower upper lower upper lower upper dsDNAmean CI CI mean CI CI mean CI CI PI 0.86 0.84 0.87 0.79 0.77 0.81 0.830.81 0.85 PII 0.87 0.85 0.88 0.80 0.77 0.82 0.81 0.79 0.83 PIII 0.830.81 0.85 0.74 0.71 0.77 0.78 0.76 0.81 PIV 0.86 0.84 0.87 0.79 0.760.82 0.83 0.81 0.85 PV 0.80 0.78 0.82 0.72 0.70 0.75 0.76 0.73 0.78 PVI0.86 0.85 0.88 0.79 0.77 0.82 0.82 0.80 0.85 Panel. 0.86 0.85 0.88 0.730.71 0.76 0.86 0.84 0.89 ENA Panel. 0.86 0.85 0.88 0.76 0.74 0.78 0.830.80 0.85 ENA + antiRib PVII 0.79 0.77 0.81 0.74 0.71 0.77 0.76 0.730.78 PVIII 0.89 0.88 0.90 0.80 0.78 0.83 0.85 0.83 0.87 PIX 0.90 0.890.92 0.81 0.79 0.83 0.85 0.83 0.87 PX 0.84 0.82 0.86 0.73 0.70 0.75 0.810.79 0.84 PXI 0.89 0.88 0.90 0.81 0.78 0.83 0.84 0.82 0.86

TABLE 9c Area under the curve (AUC), shows the sensitivity andspecificity of the different panels in the SLE cohort II. Cohort AUCSensitivity Specificity II lower upper lower upper lower upper Panelmean CI CI mean CI CI mean CI CI PI 0.84 0.83 0.86 0.74 0.72 0.76 0.790.77 0.81 PII 0.78 0.77 0.80 0.68 0.65 0.70 0.72 0.70 0.75 PIII 0.830.81 0.84 0.73 0.70 0.75 0.78 0.76 0.81 PIV 0.86 0.84 0.87 0.76 0.740.78 0.81 0.79 0.84 PV 0.77 0.75 0.78 0.67 0.65 0.69 0.74 0.72 0.76 PVI0.87 0.86 0.88 0.77 0.74 0.79 0.82 0.80 0.84 Panel. 0.76 0.74 0.77 0.590.56 0.61 78 0.75 0.80 ENA Panel. 0.84 0.83 0.86 0.73 0.71 0.76 0.830.82 0.85 ENA + antiRib PVII 0.84 0.82 0.86 0.76 0.74 0.78 0.80 0.770.82 PVIII 0.85 0.83 0.86 0.76 0.74 0.78 0.80 0.78 0.82 PIX 0.84 0.830.86 0.76 0.74 0.78 0.79 0.77 0.81 PX 0.83 0.81 0.85 0.76 0.73 0.78 0.780.76 0.80 PXI 0.82 0.81 0.84 0.74 0.71 0.76 0.79 0.76 0.81

TABLE 9d Area under the curve (AUC), sensitivity and specificity of thedifferent panels in SLE cohort II in Cohort II Panel AUC SensitivitySpecificity plus lower upper lower upper lower upper dsDNA mean CI CImean CI CI mean CI CI PI 0.84 0.82 0.85 0.73 0.71 0.76 0.78 0.76 0.81PII 0.78 0.76 0.80 0.67 0.65 0.70 0.73 0.70 0.75 PIII 0.82 0.81 0.840.73 0.71 0.75 0.76 0.74 0.79 PIV 0.85 0.84 0.87 0.76 0.73 0.78 0.800.78 0.83 PV 0.77 0.75 0.78 0.67 0.65 0.69 0.71 0.69 0.74 PVI 0.87 0.850.88 0.77 0.75 0.79 0.82 0.80 0.84 Panel. 0.77 0.76 0.79 0.60 0.58 0.630.77 0.75 0.80 ENA Panel. 0.85 0.84 0.86 0.73 0.71 0.76 0.83 0.81 0.85ENA + antiRib PVII 0.84 0.82 0.85 0.75 0.73 0.78 0.79 0.77 0.82 PVIII0.85 0.83 0.86 0.72 0.70 0.75 0.83 0.80 0.85 PIX 0.78 0.77 0.80 0.640.62 0.67 0.78 0.75 0.80 PX 0.84 0.83 0.85 0.72 0.70 0.75 0.83 0.81 0.85PXI 0.87 0.85 0.88 0.75 0.73 0.77 0.84 0.82 0.86

TABLE 9e Area under curve (AUC), sensitivity and specificity of thedifferent panels in the SLE cohort III. Cohort II Panel AUC SensitivitySpecificity plus lower upper lower upper lower upper dsDNA mean CI CImean CI CI mean CI CI PI 0.83 0.82 0.84 0.71 0.69 0.73 0.80 0.78 0.81PII 0.82 0.81 0.84 0.71 0.69 0.72 0.80 0.79 0.81 PIII 0.79 0.78 0.800.65 0.63 0.67 0.76 0.74 0.78 PIV 0.82 0.81 0.83 0.71 0.69 0.73 0.790.78 0.81 PV 0.77 0.76 0.78 0.66 0.64 0.67 0.76 0.74 0.78 PVI 0.84 0.830.85 0.71 0.70 0.73 0.81 0.79 0.82 Panel. 0.78 0.77 0.80 0.65 0.63 0.670.82 0.81 0.84 ENA Panel. 0.79 0.78 0.80 0.67 0.66 0.69 0.83 0.82 0.85ENA + antiRib PVII 0.83 0.82 0.84 0.72 0.71 0.74 0.79 0.77 0.81 PVIII0.83 0.82 0.84 0.73 0.72 0.75 0.77 0.76 0.79 PIX 0.81 0.79 0.82 0.720.70 0.74 0.76 0.74 0.77 PX 0.79 0.78 0.81 0.73 0.71 0.75 0.76 0.74 0.78PXI 0.78 0.77 0.80 0.70 0.69 0.72 0.75 0.73 0.77

FIG. 11: The figure shows the comparison of the calculated p-values andautoantibody frequencies (% positive classified observations) for theantigens from Table 2 in the three SLE cohorts. The antigens areillustrated as circles with the consecutive number. The horizontal linemarks the threshold value of p<0.05 for the comparison of SLE comparedwith healthy controls.

LITERATURE

-   Li P H, Wong W H, Lee T L, Lau C S, Chan T M, Leung A M, Tong K L,    Tse N K, Mok C C, Wong S N, Lee K W, Ho M H, Lee P P, Chong C Y,    Wong R W, Mok M Y, Ying S K, Fung S K, Lai W M, Yang W, Lau Y L.    Relationship between autoantibody clustering and clinical subsets in    SLE: cluster and association analyses in Hong Kong Chinese.    Rheumatology (Oxford). 2013 February; 52(2):337-45. doi:    10.1093/rheumatology/kes261.Epub 2012 Oct. 4. PubMed PMID: 23038697.-   Liu C C, Kao A H, Manzi S, Ahearn J M. Biomarkers in systemic lupus    erythematosus: challenges and prospects for the future. Ther Adv    Musculoskelet Dis. 2013 August; 5(4):210-33.-   Ching K H, Burbelo P D, Tipton C, Wei C, Petri M, Sanz I, Iadarola    M J. Two major autoantibody clusters in systemic lupus    erythematosus. PLoS One. 2012; 7(2):e32001. doi:    10.1371/journal.pone.0032001. Epub 2012 Feb. 21. PubMed PMID:    22363785; PubMed Central PMCID: PMC3283706.-   Stohl W. Future prospects in biologic therapy for systemic lupus    erythematosus. Nat Rev Rheumatol. 2013 Sep. 10. doi:    10.1038/nrrheum.2013.136. [Epub ahead of print] PubMed PMID:    24018550.-   Thanou A, Merrill J T. Treatment of systemic lupus erythematosus:    new therapeutic avenues and blind alleys. Nat Rev Rheumatol. 2013    Oct. 8. doi:10.1038/nrrheum.2013.145. [Epub ahead of print] PubMed    PMID: 24100460.-   Sherer Y, Gorstein A, Fritzler M J, Shoenfeld Y. Autoantibody    explosion in systemic lupus erythematosus: more than 100 different    antibodies found in SLE patients. Semin Arthritis Rheum. 2004    October; 34(2):501-37. Review. PubMed PMID: 15505768.

1-16. (canceled)
 17. A method for detection, diagnosis, differential diagnosis, prognosis, therapy control, or aftercare of systemic lupus erythematosus (SLE), comprising: a) contacting a panel of markers comprising at least one sequence selected from SEQ ID NO: 1-11, 13, 15, 16, 18, 19, 20-24, 28, 29, 31, 46, 61, 95, 126, 128, 134, 136, 143, 152, 163, 169, 171, 173, 188, 191, 213, 214, 241, 258, 270, 302, 348, 349, 367-370, 372-375, 378-391, 403, 406, 408, 415, and 423-433 with a bodily fluid or a tissue sample from an individual to be tested; b) detecting an interaction of the bodily fluid or tissue sample with at least one of the marker from step a); and c) identifying a SLE patient for stratification and administering at least one therapeutic agent to the SLE patient for treatment or monitoring the SLE patient for therapy control.
 18. The method of claim 17, wherein identifying a SLE patient for stratification comprises new or established SLE subgroups.
 19. The method of claim 17, wherein identifying a SLE patient comprises distinguishing SLE from other rheumatic diseases or other autoimmune disorders.
 20. The method of claim 17, wherein identifying a SLE patient comprises diagnosing ENA-4-negative SLE patients.
 21. The method of claim 17, wherein identifying a SLE patient comprises diagnosing lupus nephritis in SLE patients.
 22. The method of claim 17, wherein the marker sequence comprises a detection signal.
 23. The method of claim 17, wherein the detection is made by way of an antibody.
 24. The method of claim 17, wherein the body fluid is blood, blood plasma, serum, urine, cerebrospinal fluid, and/or synovial fluid.
 25. A diagnostic device or test kit comprising at least one marker for systemic lupus erythematosus selected from sequences SEQ ID NO: 1-11, 13, 15, 16, 18, 19, 20-24, 28, 29, 31, 46, 61, 95, 126, 128, 134, 136, 143, 152, 163, 169, 171, 173, 188, 191, 213, 214, 241, 258, 270, 302, 348, 349, 367-370, 372-375, 378-391, 403, 406, 408, 415, and 423-433.
 26. A panel of markers for diagnosis of systemic lupus erythematosus (SLE), comprising at least two different markers selected independently of one another from markers having the sequences of SEQ ID NO: 1-11, 13, 15, 16, 18, 19, 20-24, 28, 29, 31, 46, 61, 95, 126, 128, 134, 136, 143, 152, 163, 169, 171, 173, 188, 191, 213, 214, 241, 258, 270, 302, 348, 349, 367-370, 372-375, 378-391, 403, 406, 408, 415, and 423-433.
 27. The panel of markers for the diagnosis of SLE of claim 23, comprising at least five markers selected from the sequences of SEQ ID NO: 1-11, 13, 15, 16, 18, 19, 20-24, 28, 29, 31, 46, 61, 95, 126, 128, 134, 136, 143, 152, 163, 169, 171, 173, 188, 191, 213, 214, 241, 258, 270, 302, 348, 349, 367-370, 372-375, 378-391, 403, 406, 408, 415, and 423-433.
 28. A method for screening active substances for systemic lupus erythematosus (SLE), comprising: a) contacting a panel of markers comprising at least one sequence selected from SEQ ID NO: 1-11, 13, 15, 16, 18, 19, 20-24, 28, 29, 31, 46, 61, 95, 126, 128, 134, 136, 143, 152, 163, 169, 171, 173, 188, 191, 213, 214, 241, 258, 270, 302, 348, 349, 367-370, 372-375, 378-391, 403, 406, 408, 415, and 423-433 with a bodily fluid or a tissue sample from an individual to be tested; and b) detecting an interaction of the bodily fluid or tissue sample with at least one marker from step a). 